Starting phenix.real_space_refine on Thu Aug 6 06:27:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jpx_36489/08_2026/8jpx_36489.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpx_36489/08_2026/8jpx_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8jpx_36489/08_2026/8jpx_36489.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jpx_36489/08_2026/8jpx_36489.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jpx_36489/08_2026/8jpx_36489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpx_36489/08_2026/8jpx_36489.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpx_36489/08_2026/8jpx_36489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpx_36489/08_2026/8jpx_36489.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: 3.01, per 1000 atoms: 0.21 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: 0.80 Conformation dependent library (CDL) restraints added in 527.4 milliseconds 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: 1.70 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: 2.72 Time building geometry restraints manager: 1.23 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=" C3' DT H 16 " pdb=" C2' DT H 16 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.94e+00 bond pdb=" C3' DT G 16 " pdb=" C2' DT G 16 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.55e+00 bond pdb=" C3' DG G 12 " pdb=" C2' DG G 12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.66e+00 bond pdb=" C3' DG H 12 " pdb=" C2' DG H 12 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.09e+00 bond pdb=" C3' DT U 17 " pdb=" C2' DT U 17 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.53e+00 ... (remaining 14787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 19815 2.04 - 4.08: 407 4.08 - 6.12: 23 6.12 - 8.16: 0 8.16 - 10.20: 1 Bond angle restraints: 20246 Sorted by residual: angle pdb=" N3 DT H 13 " pdb=" C4 DT H 13 " pdb=" O4 DT H 13 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT H 6 " pdb=" C4 DT H 6 " pdb=" O4 DT H 6 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT G 6 " pdb=" C4 DT G 6 " pdb=" O4 DT G 6 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT G 13 " pdb=" C4 DT G 13 " pdb=" O4 DT G 13 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT T 17 " pdb=" C4 DT T 17 " pdb=" O4 DT T 17 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 ... (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: 1386 0.034 - 0.067: 522 0.067 - 0.101: 198 0.101 - 0.134: 117 0.134 - 0.168: 11 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=" P DT F 3 " pdb=" OP1 DT F 3 " pdb=" OP2 DT F 3 " pdb=" O5' DT F 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.15 2.00e-01 2.50e+01 5.55e-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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.280 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 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 : 0.004 0.074 14792 Z= 0.285 Angle : 0.616 10.203 20246 Z= 0.462 Chirality : 0.046 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.000 ARG B 521 TYR 0.013 0.001 TYR A 212 PHE 0.032 0.001 PHE A 439 TRP 0.006 0.001 TRP A 213 HIS 0.002 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.28 (14792) covalent geometry : angle 0.61595 / 0.46 (20246) hydrogen bonds : bond 0.15584 / 10.28 ( 575) hydrogen bonds : angle 5.68211 / 3.81 ( 1601) *********************** 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 : 0.358 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: 0.5973 time to fit residues: 112.3990 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 : 0.358 ------------------------------------------------------------------------------- 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 98 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.125895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.094610 restraints weight = 19507.028| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.22 r_work: 0.2933 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 14792 Z= 0.267 Angle : 0.648 9.006 20246 Z= 0.368 Chirality : 0.050 0.262 2234 Planarity : 0.005 0.058 2296 Dihedral : 18.289 162.003 2540 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.66 % Favored : 91.21 % Rotamer: Outliers : 3.12 % Allowed : 34.77 % Favored : 62.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.22), residues: 1536 helix: 0.65 (0.24), residues: 488 sheet: 0.93 (0.28), residues: 340 loop : -1.83 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 583 TYR 0.017 0.002 TYR A 743 PHE 0.035 0.002 PHE A 439 TRP 0.011 0.002 TRP B 222 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.27 (14792) covalent geometry : angle 0.64792 / 0.37 (20246) hydrogen bonds : bond 0.05624 / 3.67 ( 575) hydrogen bonds : angle 4.69079 / 3.18 ( 1601) *********************** 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 212 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8514 (tt) REVERT: B 162 ASP cc_start: 0.7628 (t0) cc_final: 0.7398 (t0) REVERT: B 371 GLU cc_start: 0.8171 (tp30) cc_final: 0.7697 (tt0) REVERT: B 443 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6785 (mt-10) REVERT: B 592 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8046 (pt0) REVERT: B 611 PHE cc_start: 0.6077 (m-10) cc_final: 0.5554 (m-80) REVERT: A 36 LYS cc_start: 0.7463 (ttmt) cc_final: 0.7041 (mttm) REVERT: A 150 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7938 (mt0) REVERT: A 443 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6771 (mt-10) REVERT: A 592 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8196 (pt0) outliers start: 44 outliers final: 21 residues processed: 193 average time/residue: 0.6010 time to fit residues: 125.4437 Evaluate side-chains 184 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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 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 158 LEU 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 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 563 LYS 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 83 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 12 optimal weight: 0.0770 chunk 4 optimal weight: 4.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.095749 restraints weight = 19572.318| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.25 r_work: 0.2965 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14792 Z= 0.158 Angle : 0.576 8.381 20246 Z= 0.334 Chirality : 0.046 0.244 2234 Planarity : 0.005 0.063 2296 Dihedral : 18.011 160.436 2532 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.42 % Favored : 92.45 % Rotamer: Outliers : 3.05 % Allowed : 34.70 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.22), residues: 1536 helix: 0.72 (0.24), residues: 500 sheet: 0.64 (0.27), residues: 366 loop : -1.72 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 583 TYR 0.013 0.001 TYR A 743 PHE 0.030 0.001 PHE A 439 TRP 0.009 0.001 TRP B 222 HIS 0.003 0.001 HIS B 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (14792) covalent geometry : angle 0.57556 / 0.33 (20246) hydrogen bonds : bond 0.04517 / 2.95 ( 575) hydrogen bonds : angle 4.38310 / 2.97 ( 1601) *********************** 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 212 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 371 GLU cc_start: 0.8094 (tp30) cc_final: 0.7640 (tt0) REVERT: B 443 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6845 (mt-10) REVERT: B 592 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8019 (pt0) REVERT: B 611 PHE cc_start: 0.6184 (m-10) cc_final: 0.5668 (m-80) REVERT: A 31 GLU cc_start: 0.7972 (tp30) cc_final: 0.7556 (tp30) REVERT: A 36 LYS cc_start: 0.7526 (ttmt) cc_final: 0.7022 (mttm) REVERT: A 443 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6788 (mt-10) REVERT: A 592 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8105 (pt0) outliers start: 43 outliers final: 23 residues processed: 191 average time/residue: 0.7412 time to fit residues: 153.8178 Evaluate side-chains 184 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 334 VAL 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 1 MET Chi-restraints excluded: chain A residue 14 LYS 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 407 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 709 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 64 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.094307 restraints weight = 19542.733| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.23 r_work: 0.2940 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 14792 Z= 0.218 Angle : 0.607 7.937 20246 Z= 0.347 Chirality : 0.048 0.247 2234 Planarity : 0.005 0.058 2296 Dihedral : 18.087 159.814 2532 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.14 % Favored : 91.73 % Rotamer: Outliers : 4.25 % Allowed : 34.77 % Favored : 60.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1536 helix: 0.80 (0.24), residues: 488 sheet: 0.86 (0.28), residues: 342 loop : -1.80 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 335 TYR 0.016 0.002 TYR A 743 PHE 0.033 0.002 PHE B 439 TRP 0.011 0.002 TRP A 222 HIS 0.003 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (14792) covalent geometry : angle 0.60690 / 0.35 (20246) hydrogen bonds : bond 0.04891 / 3.20 ( 575) hydrogen bonds : angle 4.37611 / 2.98 ( 1601) *********************** 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 227 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8549 (tt) REVERT: B 371 GLU cc_start: 0.8124 (tp30) cc_final: 0.7676 (tt0) REVERT: B 443 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6851 (mt-10) REVERT: B 592 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8159 (pt0) REVERT: B 611 PHE cc_start: 0.6265 (m-10) cc_final: 0.5972 (m-10) REVERT: A 36 LYS cc_start: 0.7488 (ttmt) cc_final: 0.6893 (mttm) REVERT: A 443 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6775 (mt-10) REVERT: A 592 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8233 (pt0) REVERT: A 622 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8435 (ttpt) outliers start: 60 outliers final: 33 residues processed: 206 average time/residue: 0.7323 time to fit residues: 163.4321 Evaluate side-chains 191 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET 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 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 311 ILE 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 576 PHE Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 1 MET 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 311 ILE 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 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 622 LYS 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 21 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.094450 restraints weight = 19542.856| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.22 r_work: 0.2938 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14792 Z= 0.211 Angle : 0.607 7.928 20246 Z= 0.348 Chirality : 0.047 0.248 2234 Planarity : 0.005 0.058 2296 Dihedral : 18.102 160.138 2532 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.81 % Favored : 92.06 % Rotamer: Outliers : 4.53 % Allowed : 33.85 % Favored : 61.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1536 helix: 0.83 (0.24), residues: 484 sheet: 0.83 (0.28), residues: 342 loop : -1.80 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 583 TYR 0.016 0.001 TYR B 743 PHE 0.032 0.002 PHE A 439 TRP 0.011 0.002 TRP A 222 HIS 0.003 0.001 HIS B 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (14792) covalent geometry : angle 0.60718 / 0.35 (20246) hydrogen bonds : bond 0.04808 / 3.15 ( 575) hydrogen bonds : angle 4.33601 / 2.95 ( 1601) *********************** 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 227 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8581 (tt) REVERT: B 162 ASP cc_start: 0.7619 (t0) cc_final: 0.7350 (t0) REVERT: B 168 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8424 (mt-10) REVERT: B 371 GLU cc_start: 0.8150 (tp30) cc_final: 0.7704 (tt0) REVERT: B 443 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6844 (mt-10) REVERT: B 592 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: A 36 LYS cc_start: 0.7481 (ttmt) cc_final: 0.6892 (mttm) REVERT: A 443 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6801 (mt-10) REVERT: A 458 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: A 592 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8182 (pt0) REVERT: A 622 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8477 (ttpt) outliers start: 64 outliers final: 39 residues processed: 207 average time/residue: 0.6748 time to fit residues: 152.3141 Evaluate side-chains 201 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 78 ILE 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 311 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 592 GLU 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 238 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.095993 restraints weight = 19497.245| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.24 r_work: 0.2953 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14792 Z= 0.146 Angle : 0.569 7.460 20246 Z= 0.330 Chirality : 0.046 0.236 2234 Planarity : 0.005 0.057 2296 Dihedral : 18.060 160.965 2532 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.62 % Favored : 92.25 % Rotamer: Outliers : 3.90 % Allowed : 34.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.22), residues: 1536 helix: 0.84 (0.24), residues: 496 sheet: 0.61 (0.27), residues: 366 loop : -1.71 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 583 TYR 0.012 0.001 TYR A 212 PHE 0.030 0.001 PHE A 439 TRP 0.011 0.001 TRP B 222 HIS 0.002 0.001 HIS B 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (14792) covalent geometry : angle 0.56915 / 0.33 (20246) hydrogen bonds : bond 0.04206 / 2.76 ( 575) hydrogen bonds : angle 4.20790 / 2.86 ( 1601) *********************** 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 224 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8525 (tt) REVERT: B 371 GLU cc_start: 0.8144 (tp30) cc_final: 0.7642 (tt0) REVERT: B 440 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.5811 (tpt170) REVERT: B 443 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6923 (mt-10) REVERT: B 611 PHE cc_start: 0.6430 (m-10) cc_final: 0.6139 (m-10) REVERT: A 36 LYS cc_start: 0.7435 (ttmt) cc_final: 0.6854 (mttm) REVERT: A 443 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6811 (mt-10) REVERT: A 458 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: A 592 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8120 (pt0) REVERT: A 622 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8518 (ttpt) outliers start: 55 outliers final: 31 residues processed: 208 average time/residue: 0.7522 time to fit residues: 169.5271 Evaluate side-chains 193 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 78 ILE 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 345 SER Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 709 LYS 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 126 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 499 ASN A 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.096088 restraints weight = 19319.739| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.23 r_work: 0.2963 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14792 Z= 0.155 Angle : 0.572 7.266 20246 Z= 0.331 Chirality : 0.046 0.235 2234 Planarity : 0.005 0.056 2296 Dihedral : 18.029 160.662 2532 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.88 % Favored : 91.99 % Rotamer: Outliers : 3.97 % Allowed : 34.99 % Favored : 61.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.22), residues: 1536 helix: 0.85 (0.24), residues: 496 sheet: 0.62 (0.27), residues: 378 loop : -1.73 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 521 TYR 0.012 0.001 TYR B 743 PHE 0.030 0.001 PHE A 439 TRP 0.010 0.001 TRP A 222 HIS 0.003 0.001 HIS B 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (14792) covalent geometry : angle 0.57228 / 0.33 (20246) hydrogen bonds : bond 0.04183 / 2.75 ( 575) hydrogen bonds : angle 4.17726 / 2.84 ( 1601) *********************** 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 223 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8545 (tt) REVERT: B 168 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8408 (mt-10) REVERT: B 204 ASP cc_start: 0.8372 (t0) cc_final: 0.8168 (t0) REVERT: B 371 GLU cc_start: 0.8229 (tp30) cc_final: 0.7780 (tt0) REVERT: B 440 ARG cc_start: 0.6315 (OUTLIER) cc_final: 0.5911 (tpt170) REVERT: B 443 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6923 (mt-10) REVERT: B 592 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8138 (pt0) REVERT: A 36 LYS cc_start: 0.7464 (ttmt) cc_final: 0.6885 (mttm) REVERT: A 204 ASP cc_start: 0.8373 (t0) cc_final: 0.8170 (t0) REVERT: A 358 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7941 (p) REVERT: A 443 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6800 (mt-10) REVERT: A 458 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: A 592 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8106 (pt0) REVERT: A 622 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8554 (ttpt) outliers start: 56 outliers final: 34 residues processed: 204 average time/residue: 0.7066 time to fit residues: 157.1100 Evaluate side-chains 200 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 345 SER Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 709 LYS 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 100 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 123 optimal weight: 0.0370 chunk 75 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 499 ASN A 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.093729 restraints weight = 19362.202| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.24 r_work: 0.2937 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 14792 Z= 0.247 Angle : 0.631 7.224 20246 Z= 0.358 Chirality : 0.049 0.247 2234 Planarity : 0.005 0.056 2296 Dihedral : 18.030 159.385 2530 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.33 % Favored : 91.54 % Rotamer: Outliers : 3.97 % Allowed : 34.99 % Favored : 61.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.22), residues: 1536 helix: 0.68 (0.24), residues: 496 sheet: 0.93 (0.28), residues: 350 loop : -1.91 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 521 TYR 0.017 0.002 TYR A 743 PHE 0.031 0.002 PHE A 439 TRP 0.012 0.002 TRP B 222 HIS 0.004 0.001 HIS B 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.25 (14792) covalent geometry : angle 0.63059 / 0.36 (20246) hydrogen bonds : bond 0.04923 / 3.23 ( 575) hydrogen bonds : angle 4.30328 / 2.94 ( 1601) *********************** 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 215 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8609 (tt) REVERT: B 162 ASP cc_start: 0.7610 (t0) cc_final: 0.7339 (t0) REVERT: B 371 GLU cc_start: 0.8190 (tp30) cc_final: 0.7741 (tt0) REVERT: B 440 ARG cc_start: 0.6482 (OUTLIER) cc_final: 0.5768 (mpt180) REVERT: B 443 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6825 (mt-10) REVERT: B 592 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: B 630 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8188 (ptm160) REVERT: A 36 LYS cc_start: 0.7506 (ttmt) cc_final: 0.6906 (mttm) REVERT: A 358 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7895 (p) REVERT: A 443 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6811 (mt-10) REVERT: A 458 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: A 592 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8297 (pt0) REVERT: A 622 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8481 (ttpt) outliers start: 56 outliers final: 35 residues processed: 197 average time/residue: 0.7444 time to fit residues: 159.4281 Evaluate side-chains 199 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 630 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 622 LYS 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 142 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 749 ASN A 749 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.128293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.097183 restraints weight = 19519.464| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.23 r_work: 0.2954 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1045 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= 0.142 Angle : 0.577 7.206 20246 Z= 0.333 Chirality : 0.046 0.233 2234 Planarity : 0.005 0.055 2296 Dihedral : 18.013 160.536 2530 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.36 % Favored : 92.51 % Rotamer: Outliers : 3.26 % Allowed : 35.91 % Favored : 60.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.22), residues: 1536 helix: 0.84 (0.24), residues: 496 sheet: 0.82 (0.27), residues: 360 loop : -1.83 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 521 TYR 0.012 0.001 TYR A 212 PHE 0.030 0.001 PHE A 439 TRP 0.011 0.001 TRP A 222 HIS 0.002 0.001 HIS B 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (14792) covalent geometry : angle 0.57716 / 0.33 (20246) hydrogen bonds : bond 0.04185 / 2.74 ( 575) hydrogen bonds : angle 4.18084 / 2.84 ( 1601) *********************** 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 209 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8570 (tt) REVERT: B 371 GLU cc_start: 0.8185 (tp30) cc_final: 0.7698 (tt0) REVERT: B 440 ARG cc_start: 0.6360 (OUTLIER) cc_final: 0.5867 (tpt170) REVERT: B 443 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6903 (mt-10) REVERT: B 458 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: B 592 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7998 (pt0) REVERT: A 36 LYS cc_start: 0.7465 (ttmt) cc_final: 0.6872 (mttm) REVERT: A 358 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7921 (p) REVERT: A 443 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 458 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: A 583 ARG cc_start: 0.7192 (mtp85) cc_final: 0.6990 (mmp80) REVERT: A 592 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8099 (pt0) REVERT: A 622 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8364 (ttpt) outliers start: 46 outliers final: 31 residues processed: 194 average time/residue: 0.6945 time to fit residues: 146.3664 Evaluate side-chains 191 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET 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 345 SER Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 592 GLU 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 241 LYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 48 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 140 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.127433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.096087 restraints weight = 19321.541| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.23 r_work: 0.2963 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14792 Z= 0.153 Angle : 0.586 7.092 20246 Z= 0.338 Chirality : 0.046 0.234 2234 Planarity : 0.005 0.056 2296 Dihedral : 18.028 160.471 2530 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.68 % Favored : 92.19 % Rotamer: Outliers : 3.05 % Allowed : 36.26 % Favored : 60.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.22), residues: 1536 helix: 0.81 (0.24), residues: 500 sheet: 0.62 (0.27), residues: 378 loop : -1.72 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 521 TYR 0.012 0.001 TYR B 743 PHE 0.031 0.001 PHE A 439 TRP 0.014 0.001 TRP A 222 HIS 0.002 0.001 HIS A 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (14792) covalent geometry : angle 0.58576 / 0.34 (20246) hydrogen bonds : bond 0.04132 / 2.72 ( 575) hydrogen bonds : angle 4.13855 / 2.81 ( 1601) ********************** 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 203 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8572 (tt) REVERT: B 371 GLU cc_start: 0.8229 (tp30) cc_final: 0.7769 (tt0) REVERT: B 440 ARG cc_start: 0.6359 (OUTLIER) cc_final: 0.5849 (tpt170) REVERT: B 443 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6901 (mt-10) REVERT: B 458 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: A 31 GLU cc_start: 0.8157 (tp30) cc_final: 0.7951 (tp30) REVERT: A 36 LYS cc_start: 0.7479 (ttmt) cc_final: 0.6956 (mttm) REVERT: A 358 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7947 (p) REVERT: A 443 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6770 (mt-10) REVERT: A 458 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: A 592 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8079 (pt0) outliers start: 43 outliers final: 30 residues processed: 188 average time/residue: 0.7222 time to fit residues: 147.7362 Evaluate side-chains 190 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 679 LEU 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 241 LYS Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 143 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.095121 restraints weight = 19431.383| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.21 r_work: 0.2948 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14792 Z= 0.191 Angle : 0.607 7.555 20246 Z= 0.348 Chirality : 0.047 0.238 2234 Planarity : 0.005 0.083 2296 Dihedral : 18.020 159.654 2528 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.81 % Favored : 91.93 % Rotamer: Outliers : 2.90 % Allowed : 36.61 % Favored : 60.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.22), residues: 1536 helix: 0.93 (0.24), residues: 488 sheet: 0.58 (0.27), residues: 382 loop : -1.78 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 521 TYR 0.014 0.001 TYR B 743 PHE 0.031 0.002 PHE A 439 TRP 0.013 0.002 TRP A 222 HIS 0.003 0.001 HIS B 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (14792) covalent geometry : angle 0.60692 / 0.35 (20246) hydrogen bonds : bond 0.04477 / 2.93 ( 575) hydrogen bonds : angle 4.18481 / 2.85 ( 1601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4791.85 seconds wall clock time: 82 minutes 23.07 seconds (4943.07 seconds total)