Starting phenix.real_space_refine on Fri Aug 1 00:00:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpx_36489/07_2025/8jpx_36489.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpx_36489/07_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_36489/07_2025/8jpx_36489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpx_36489/07_2025/8jpx_36489.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpx_36489/07_2025/8jpx_36489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpx_36489/07_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 10.78, per 1000 atoms: 0.75 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: 5.63 Conformation dependent library (CDL) restraints added in 3.8 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: 8.70 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: 13.03 Time building geometry restraints manager: 5.49 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: 87.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 56.530 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:101.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 246.700 ------------------------------------------------------------------------------- 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 : 2.025 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: 1.8601 time to fit residues: 348.9486 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 : 1.548 ------------------------------------------------------------------------------- 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 = 0.128213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.097029 restraints weight = 19256.446| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.21 r_work: 0.2968 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 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 : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 371 GLU cc_start: 0.8134 (tp30) cc_final: 0.7626 (tt0) REVERT: B 443 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6805 (mt-10) REVERT: B 592 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7994 (pt0) REVERT: B 611 PHE cc_start: 0.6167 (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: 0.7373 (ttmt) cc_final: 0.7018 (mttm) REVERT: A 150 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: A 443 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6782 (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: 2.1609 time to fit residues: 457.2339 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 : 1.789 ------------------------------------------------------------------------------- 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: 9.9990 chunk 151 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 111 optimal weight: 0.0570 chunk 109 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.128667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.097529 restraints weight = 19370.117| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.22 r_work: 0.2973 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14792 Z= 0.160 Angle : 0.548 8.050 20246 Z= 0.307 Chirality : 0.044 0.138 2234 Planarity : 0.004 0.055 2296 Dihedral : 17.994 157.145 2532 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.38 % Rotamer: Outliers : 3.33 % Allowed : 34.77 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.22), residues: 1536 helix: 1.03 (0.25), residues: 488 sheet: 0.65 (0.27), residues: 378 loop : -1.67 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 222 HIS 0.002 0.001 HIS A 742 PHE 0.028 0.001 PHE A 439 TYR 0.012 0.001 TYR A 743 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 575) hydrogen bonds : angle 4.18727 ( 1601) covalent geometry : bond 0.00373 (14792) covalent geometry : angle 0.54791 (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 219 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 371 GLU cc_start: 0.8156 (tp30) cc_final: 0.7664 (tt0) REVERT: B 443 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6856 (mt-10) REVERT: B 592 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8098 (pt0) REVERT: B 611 PHE cc_start: 0.6269 (m-10) cc_final: 0.5940 (m-10) REVERT: B 635 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8734 (mt-10) REVERT: A 31 GLU cc_start: 0.8045 (tp30) cc_final: 0.7803 (tp30) REVERT: A 36 LYS cc_start: 0.7363 (ttmt) cc_final: 0.7013 (mttm) REVERT: A 443 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6797 (mm-30) REVERT: A 592 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8088 (pt0) REVERT: A 622 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8577 (ttpt) REVERT: A 635 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8729 (mt-10) outliers start: 47 outliers final: 26 residues processed: 202 average time/residue: 2.5581 time to fit residues: 558.1618 Evaluate side-chains 192 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 310 ASP 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 576 PHE Chi-restraints excluded: chain B residue 592 GLU 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 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 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 622 LYS 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: 1.9990 chunk 92 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 97 optimal weight: 0.0470 chunk 53 optimal weight: 10.0000 chunk 9 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 overall best weight: 1.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.130135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.099064 restraints weight = 19294.429| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.21 r_work: 0.2994 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14792 Z= 0.135 Angle : 0.528 7.286 20246 Z= 0.297 Chirality : 0.043 0.140 2234 Planarity : 0.004 0.055 2296 Dihedral : 17.979 156.816 2532 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.16 % Favored : 92.71 % Rotamer: Outliers : 3.54 % Allowed : 34.92 % Favored : 61.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1536 helix: 0.99 (0.24), residues: 500 sheet: 0.81 (0.27), residues: 354 loop : -1.64 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 222 HIS 0.002 0.001 HIS B 144 PHE 0.027 0.001 PHE A 439 TYR 0.011 0.001 TYR B 212 ARG 0.007 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 575) hydrogen bonds : angle 4.04572 ( 1601) covalent geometry : bond 0.00307 (14792) covalent geometry : angle 0.52806 (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 230 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8495 (tt) REVERT: B 287 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7805 (tm-30) REVERT: B 371 GLU cc_start: 0.8145 (tp30) cc_final: 0.7668 (tt0) REVERT: B 443 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6911 (mt-10) REVERT: B 611 PHE cc_start: 0.6391 (m-10) cc_final: 0.6008 (m-10) REVERT: B 635 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8713 (mt-10) REVERT: A 31 GLU cc_start: 0.8095 (tp30) cc_final: 0.7882 (tp30) REVERT: A 36 LYS cc_start: 0.7327 (ttmt) cc_final: 0.6979 (mttm) REVERT: A 287 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 443 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6790 (mm-30) REVERT: A 635 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8726 (mt-10) outliers start: 50 outliers final: 28 residues processed: 212 average time/residue: 1.6645 time to fit residues: 380.9431 Evaluate side-chains 193 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 499 ASN 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 407 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 576 PHE 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=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: 6.9990 chunk 120 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.093846 restraints weight = 19615.003| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.24 r_work: 0.2932 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14792 Z= 0.232 Angle : 0.605 8.051 20246 Z= 0.336 Chirality : 0.046 0.145 2234 Planarity : 0.005 0.056 2296 Dihedral : 18.103 156.263 2530 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.88 % Favored : 91.99 % Rotamer: Outliers : 3.97 % Allowed : 34.77 % Favored : 61.26 % 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: -0.37 (0.22), residues: 1536 helix: 0.99 (0.24), residues: 484 sheet: 0.88 (0.28), residues: 346 loop : -1.78 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 222 HIS 0.003 0.001 HIS A 742 PHE 0.033 0.002 PHE B 439 TYR 0.018 0.002 TYR B 743 ARG 0.007 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04791 ( 575) hydrogen bonds : angle 4.26944 ( 1601) covalent geometry : bond 0.00555 (14792) covalent geometry : angle 0.60523 (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 223 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8565 (tt) REVERT: B 162 ASP cc_start: 0.7763 (t0) cc_final: 0.7492 (t0) REVERT: B 371 GLU cc_start: 0.8099 (tp30) cc_final: 0.7618 (tt0) REVERT: B 440 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.6151 (tpt170) REVERT: B 443 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6895 (mt-10) REVERT: B 523 ASP cc_start: 0.8221 (t0) cc_final: 0.8010 (t0) REVERT: A 31 GLU cc_start: 0.8168 (tp30) cc_final: 0.7958 (tp30) REVERT: A 36 LYS cc_start: 0.7383 (ttmt) cc_final: 0.6935 (mttm) REVERT: A 443 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6880 (mt-10) REVERT: A 458 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: A 523 ASP cc_start: 0.8222 (t0) cc_final: 0.8012 (t0) outliers start: 56 outliers final: 31 residues processed: 206 average time/residue: 1.5889 time to fit residues: 352.9957 Evaluate side-chains 191 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 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 310 ASP Chi-restraints excluded: chain A residue 334 VAL 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 499 ASN Chi-restraints excluded: chain A residue 576 PHE 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: 4.9990 chunk 88 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 0.0980 chunk 140 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 499 ASN A 99 ASN A 499 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.099394 restraints weight = 19483.680| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.24 r_work: 0.3017 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14792 Z= 0.116 Angle : 0.520 6.074 20246 Z= 0.294 Chirality : 0.043 0.141 2234 Planarity : 0.004 0.053 2296 Dihedral : 17.964 157.517 2530 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.58 % Favored : 93.29 % Rotamer: Outliers : 2.90 % Allowed : 36.83 % Favored : 60.27 % 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: -0.21 (0.22), residues: 1536 helix: 0.92 (0.24), residues: 512 sheet: 0.97 (0.28), residues: 340 loop : -1.60 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 222 HIS 0.002 0.000 HIS B 144 PHE 0.027 0.001 PHE A 439 TYR 0.012 0.001 TYR B 212 ARG 0.005 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 575) hydrogen bonds : angle 3.90020 ( 1601) covalent geometry : bond 0.00252 (14792) covalent geometry : angle 0.52025 (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: 41 poor density : 178 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8511 (tt) REVERT: B 287 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 371 GLU cc_start: 0.8215 (tp30) cc_final: 0.7740 (tt0) REVERT: B 375 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7996 (mtpp) REVERT: B 440 ARG cc_start: 0.6259 (OUTLIER) cc_final: 0.5939 (tpt170) REVERT: B 443 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6921 (mt-10) REVERT: B 611 PHE cc_start: 0.7022 (m-10) cc_final: 0.6764 (m-10) REVERT: A 31 GLU cc_start: 0.8139 (tp30) cc_final: 0.7683 (tp30) REVERT: A 32 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8422 (mm-30) REVERT: A 36 LYS cc_start: 0.7352 (ttmt) cc_final: 0.6978 (mttm) REVERT: A 287 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 443 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6836 (mm-30) REVERT: A 458 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8017 (mt-10) outliers start: 41 outliers final: 23 residues processed: 206 average time/residue: 1.5641 time to fit residues: 348.5066 Evaluate side-chains 191 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 232 TYR Chi-restraints excluded: chain B residue 241 LYS 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 499 ASN 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 232 TYR 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 616 ILE 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: 9.9990 chunk 118 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 5 optimal weight: 0.0770 chunk 32 optimal weight: 5.9990 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 499 ASN A 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.094196 restraints weight = 19682.457| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.23 r_work: 0.2925 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 14792 Z= 0.268 Angle : 0.634 7.750 20246 Z= 0.351 Chirality : 0.048 0.150 2234 Planarity : 0.005 0.054 2296 Dihedral : 18.149 155.493 2530 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.01 % Favored : 91.86 % Rotamer: Outliers : 3.90 % Allowed : 35.84 % Favored : 60.27 % 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: -0.46 (0.22), residues: 1536 helix: 0.73 (0.24), residues: 502 sheet: 0.97 (0.28), residues: 350 loop : -1.86 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 222 HIS 0.003 0.001 HIS B 742 PHE 0.034 0.002 PHE B 439 TYR 0.019 0.002 TYR A 743 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.05131 ( 575) hydrogen bonds : angle 4.31284 ( 1601) covalent geometry : bond 0.00645 (14792) covalent geometry : angle 0.63353 (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: 55 poor density : 165 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8540 (tt) REVERT: B 162 ASP cc_start: 0.7830 (t0) cc_final: 0.7568 (t0) REVERT: B 371 GLU cc_start: 0.8096 (tp30) cc_final: 0.7615 (tt0) REVERT: B 440 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.6169 (tpt170) REVERT: B 523 ASP cc_start: 0.8273 (t0) cc_final: 0.8064 (t0) REVERT: A 31 GLU cc_start: 0.8191 (tp30) cc_final: 0.7742 (tp30) REVERT: A 32 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8453 (mm-30) REVERT: A 36 LYS cc_start: 0.7429 (ttmt) cc_final: 0.6975 (mttm) REVERT: A 443 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6903 (mt-10) REVERT: A 458 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: A 523 ASP cc_start: 0.8254 (t0) cc_final: 0.8044 (t0) REVERT: A 592 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8287 (pt0) outliers start: 55 outliers final: 24 residues processed: 201 average time/residue: 1.5990 time to fit residues: 346.4998 Evaluate side-chains 188 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 311 ILE 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 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 311 ILE 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 592 GLU 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: 6.9990 chunk 50 optimal weight: 4.9990 chunk 140 optimal weight: 0.0020 chunk 88 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 115 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 749 ASN A 99 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 = 0.3557 r_free = 0.3557 target = 0.132345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.101366 restraints weight = 19488.761| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.24 r_work: 0.3036 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14792 Z= 0.111 Angle : 0.521 6.666 20246 Z= 0.295 Chirality : 0.043 0.172 2234 Planarity : 0.004 0.053 2296 Dihedral : 17.983 157.163 2530 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.10 % Rotamer: Outliers : 2.27 % Allowed : 37.68 % Favored : 60.06 % 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: -0.13 (0.22), residues: 1536 helix: 1.14 (0.24), residues: 502 sheet: 1.29 (0.29), residues: 322 loop : -1.74 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 222 HIS 0.002 0.000 HIS B 742 PHE 0.027 0.001 PHE A 439 TYR 0.015 0.001 TYR A 212 ARG 0.005 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 575) hydrogen bonds : angle 3.84357 ( 1601) covalent geometry : bond 0.00237 (14792) covalent geometry : angle 0.52100 (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 206 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7756 (tm-30) REVERT: B 371 GLU cc_start: 0.8189 (tp30) cc_final: 0.7724 (tt0) REVERT: B 440 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.6015 (tpt170) REVERT: B 443 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6928 (mt-10) REVERT: B 611 PHE cc_start: 0.7522 (m-10) cc_final: 0.7315 (m-10) REVERT: A 31 GLU cc_start: 0.8176 (tp30) cc_final: 0.7702 (tp30) REVERT: A 32 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8393 (mm-30) REVERT: A 36 LYS cc_start: 0.7346 (ttmt) cc_final: 0.6995 (mttm) REVERT: A 287 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7738 (tm-30) REVERT: A 443 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6815 (mm-30) REVERT: A 458 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8029 (mt-10) outliers start: 32 outliers final: 18 residues processed: 195 average time/residue: 1.5556 time to fit residues: 327.1320 Evaluate side-chains 182 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 156 TRP Chi-restraints excluded: chain B residue 157 GLU 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 407 LEU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 457 ILE 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 232 TYR Chi-restraints excluded: chain A residue 310 ASP 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 770 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 63 optimal weight: 0.3980 chunk 115 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 99 optimal weight: 0.0370 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 123 optimal weight: 0.1980 chunk 145 optimal weight: 4.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN B 503 GLN A 99 ASN A 499 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.100451 restraints weight = 19430.926| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.23 r_work: 0.3017 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14792 Z= 0.126 Angle : 0.533 6.812 20246 Z= 0.300 Chirality : 0.043 0.154 2234 Planarity : 0.004 0.069 2296 Dihedral : 17.946 155.253 2530 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.84 % Favored : 93.03 % Rotamer: Outliers : 1.98 % Allowed : 38.03 % Favored : 59.99 % 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: -0.07 (0.22), residues: 1536 helix: 1.23 (0.24), residues: 502 sheet: 1.32 (0.29), residues: 326 loop : -1.75 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 222 HIS 0.002 0.001 HIS B 144 PHE 0.025 0.001 PHE A 439 TYR 0.013 0.001 TYR A 212 ARG 0.005 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 575) hydrogen bonds : angle 3.84688 ( 1601) covalent geometry : bond 0.00282 (14792) covalent geometry : angle 0.53290 (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 191 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8512 (tt) REVERT: B 287 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7840 (tm-30) REVERT: B 371 GLU cc_start: 0.8180 (tp30) cc_final: 0.7720 (tt0) REVERT: B 443 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6915 (mt-10) REVERT: B 458 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: A 31 GLU cc_start: 0.8173 (tp30) cc_final: 0.7706 (tp30) REVERT: A 32 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8399 (mm-30) REVERT: A 36 LYS cc_start: 0.7346 (ttmt) cc_final: 0.6946 (mttm) REVERT: A 287 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7807 (tm-30) REVERT: A 443 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6773 (mm-30) REVERT: A 458 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8043 (mt-10) outliers start: 28 outliers final: 18 residues processed: 178 average time/residue: 2.2139 time to fit residues: 426.4141 Evaluate side-chains 182 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 2.693 ------------------------------------------------------------------------------- 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 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 407 LEU 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 679 LEU Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 310 ASP 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 679 LEU 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: 1.9990 chunk 27 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 499 ASN A 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.098676 restraints weight = 19428.337| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.23 r_work: 0.2986 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14792 Z= 0.159 Angle : 0.553 7.171 20246 Z= 0.310 Chirality : 0.044 0.148 2234 Planarity : 0.004 0.056 2296 Dihedral : 17.929 154.425 2528 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.55 % Favored : 92.32 % Rotamer: Outliers : 1.98 % Allowed : 37.96 % Favored : 60.06 % 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: -0.13 (0.22), residues: 1536 helix: 1.15 (0.24), residues: 504 sheet: 1.31 (0.29), residues: 322 loop : -1.77 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 222 HIS 0.002 0.001 HIS B 144 PHE 0.025 0.001 PHE B 439 TYR 0.012 0.001 TYR A 743 ARG 0.004 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 575) hydrogen bonds : angle 3.93053 ( 1601) covalent geometry : bond 0.00369 (14792) covalent geometry : angle 0.55276 (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 189 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8511 (tt) REVERT: B 287 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7801 (tm-30) REVERT: B 371 GLU cc_start: 0.8144 (tp30) cc_final: 0.7669 (tt0) REVERT: B 443 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6901 (mt-10) REVERT: A 31 GLU cc_start: 0.8171 (tp30) cc_final: 0.7703 (tp30) REVERT: A 32 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8400 (mm-30) REVERT: A 36 LYS cc_start: 0.7376 (ttmt) cc_final: 0.6962 (mttm) REVERT: A 287 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 443 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6772 (mm-30) REVERT: A 458 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: A 592 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8099 (pt0) outliers start: 28 outliers final: 22 residues processed: 178 average time/residue: 1.6580 time to fit residues: 317.3598 Evaluate side-chains 180 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 770 VAL 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 232 TYR Chi-restraints excluded: chain A residue 241 LYS 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 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 679 LEU 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: 8.9990 chunk 1 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.095132 restraints weight = 19599.368| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.24 r_work: 0.2943 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14792 Z= 0.240 Angle : 0.619 7.454 20246 Z= 0.345 Chirality : 0.047 0.150 2234 Planarity : 0.005 0.052 2296 Dihedral : 18.070 154.485 2528 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.55 % Favored : 92.32 % Rotamer: Outliers : 2.20 % Allowed : 37.68 % Favored : 60.13 % 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: 0.89 (0.24), residues: 502 sheet: 1.03 (0.28), residues: 350 loop : -1.84 (0.24), residues: 684 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 0.032 0.002 PHE B 439 TYR 0.017 0.002 TYR A 743 ARG 0.005 0.000 ARG B 380 Details of bonding type rmsd hydrogen bonds : bond 0.04747 ( 575) hydrogen bonds : angle 4.20205 ( 1601) covalent geometry : bond 0.00575 (14792) covalent geometry : angle 0.61914 (20246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11770.92 seconds wall clock time: 213 minutes 8.00 seconds (12788.00 seconds total)