Starting phenix.real_space_refine on Sat Oct 11 10:43:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpx_36489/10_2025/8jpx_36489.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpx_36489/10_2025/8jpx_36489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jpx_36489/10_2025/8jpx_36489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpx_36489/10_2025/8jpx_36489.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpx_36489/10_2025/8jpx_36489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpx_36489/10_2025/8jpx_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/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: 3.73, per 1000 atoms: 0.26 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: 1.25 Conformation dependent library (CDL) restraints added in 587.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.25 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: 2.84 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3610 1.33 - 1.45: 2848 1.45 - 1.57: 8108 1.57 - 1.69: 152 1.69 - 1.81: 74 Bond restraints: 14792 Sorted by residual: bond pdb=" CB PRO B 185 " pdb=" CG PRO B 185 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.20e+00 bond pdb=" C LEU B 263 " pdb=" N LEU B 264 " ideal model delta sigma weight residual 1.328 1.305 0.023 1.67e-02 3.59e+03 1.83e+00 bond pdb=" CB ASP B 310 " pdb=" CG ASP B 310 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.22e+00 bond pdb=" O4' DG H 15 " pdb=" C1' DG H 15 " ideal model delta sigma weight residual 1.414 1.395 0.019 2.00e-02 2.50e+03 9.01e-01 bond pdb=" C4' DG G 12 " pdb=" O4' DG G 12 " ideal model delta sigma weight residual 1.450 1.431 0.019 2.00e-02 2.50e+03 8.98e-01 ... (remaining 14787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 19930 2.04 - 4.08: 292 4.08 - 6.12: 23 6.12 - 8.16: 0 8.16 - 10.20: 1 Bond angle restraints: 20246 Sorted by residual: angle pdb=" N LEU A 158 " pdb=" CA LEU A 158 " pdb=" C LEU A 158 " ideal model delta sigma weight residual 114.62 109.88 4.74 1.14e+00 7.69e-01 1.73e+01 angle pdb=" N LEU B 158 " pdb=" CA LEU B 158 " pdb=" C LEU B 158 " ideal model delta sigma weight residual 114.62 109.94 4.68 1.14e+00 7.69e-01 1.69e+01 angle pdb=" CA LEU A 158 " pdb=" C LEU A 158 " pdb=" N VAL A 159 " ideal model delta sigma weight residual 119.71 116.28 3.43 1.17e+00 7.31e-01 8.62e+00 angle pdb=" CA LEU B 158 " pdb=" C LEU B 158 " pdb=" N VAL B 159 " ideal model delta sigma weight residual 119.71 116.35 3.36 1.17e+00 7.31e-01 8.27e+00 angle pdb=" C ASP B 577 " pdb=" N SER B 578 " pdb=" CA SER B 578 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.26e+00 ... (remaining 20241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.45: 8043 31.45 - 62.90: 780 62.90 - 94.34: 43 94.34 - 125.79: 0 125.79 - 157.24: 4 Dihedral angle restraints: 8870 sinusoidal: 4294 harmonic: 4576 Sorted by residual: dihedral pdb=" C4' DT F 2 " pdb=" C3' DT F 2 " pdb=" O3' DT F 2 " pdb=" P DT F 3 " ideal model delta sinusoidal sigma weight residual 220.00 62.76 157.24 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DT E 2 " pdb=" C3' DT E 2 " pdb=" O3' DT E 2 " pdb=" P DT E 3 " ideal model delta sinusoidal sigma weight residual 220.00 76.92 143.08 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" CA ASP B 438 " pdb=" C ASP B 438 " pdb=" N PHE B 439 " pdb=" CA PHE B 439 " ideal model delta harmonic sigma weight residual -180.00 -161.58 -18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 8867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1468 0.034 - 0.067: 503 0.067 - 0.101: 153 0.101 - 0.134: 104 0.134 - 0.168: 6 Chirality restraints: 2234 Sorted by residual: chirality pdb=" CB ILE B 616 " pdb=" CA ILE B 616 " pdb=" CG1 ILE B 616 " pdb=" CG2 ILE B 616 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CB ILE A 616 " pdb=" CA ILE A 616 " pdb=" CG1 ILE A 616 " pdb=" CG2 ILE A 616 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE B 694 " pdb=" N ILE B 694 " pdb=" C ILE B 694 " pdb=" CB ILE B 694 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 2231 not shown) Planarity restraints: 2296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 583 " 0.237 9.50e-02 1.11e+02 1.06e-01 7.02e+00 pdb=" NE ARG B 583 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 583 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 583 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 583 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 162 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO B 163 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 163 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 163 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 29 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO B 30 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.028 5.00e-02 4.00e+02 ... (remaining 2293 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 56 2.50 - 3.10: 9340 3.10 - 3.70: 20429 3.70 - 4.30: 31713 4.30 - 4.90: 53439 Nonbonded interactions: 114977 Sorted by model distance: nonbonded pdb=" OP1 DT U 10 " pdb="MG MG B 801 " model vdw 1.900 2.170 nonbonded pdb=" OP1 DT T 10 " pdb="MG MG A 801 " model vdw 1.900 2.170 nonbonded pdb=" OD2 ASP A 558 " pdb="MG MG A 801 " model vdw 1.900 2.170 nonbonded pdb=" OD2 ASP B 558 " pdb="MG MG B 801 " model vdw 1.903 2.170 nonbonded pdb=" ND1 HIS A 745 " pdb="MG MG A 801 " model vdw 2.008 2.250 ... (remaining 114972 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.390 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:7.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14792 Z= 0.141 Angle : 0.562 10.203 20246 Z= 0.322 Chirality : 0.043 0.168 2234 Planarity : 0.005 0.106 2296 Dihedral : 21.049 157.240 5914 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.50 % Allowed : 34.07 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (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 covalent geometry : bond 0.00316 (14792) covalent geometry : angle 0.56157 (20246) hydrogen bonds : bond 0.15584 ( 575) hydrogen bonds : angle 5.68211 ( 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 : 0.644 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: 0.7909 time to fit residues: 148.1347 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 : 0.558 ------------------------------------------------------------------------------- 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: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: B 672 ASN A 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.092622 restraints weight = 19563.275| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.23 r_work: 0.2913 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 14792 Z= 0.285 Angle : 0.647 9.542 20246 Z= 0.358 Chirality : 0.048 0.151 2234 Planarity : 0.005 0.056 2296 Dihedral : 18.471 165.091 2540 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.53 % Favored : 91.34 % Rotamer: Outliers : 3.61 % Allowed : 34.14 % 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 aren not related in a simple way. whole: -0.64 (0.22), residues: 1536 helix: 0.61 (0.24), residues: 488 sheet: 0.55 (0.27), residues: 366 loop : -1.78 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 583 TYR 0.020 0.002 TYR B 743 PHE 0.036 0.002 PHE B 439 TRP 0.011 0.002 TRP B 222 HIS 0.003 0.001 HIS B 742 Details of bonding type rmsd covalent geometry : bond 0.00689 (14792) covalent geometry : angle 0.64680 (20246) hydrogen bonds : bond 0.05415 ( 575) hydrogen bonds : angle 4.64722 ( 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 216 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8656 (tt) REVERT: B 162 ASP cc_start: 0.7764 (t0) cc_final: 0.7556 (t0) REVERT: B 371 GLU cc_start: 0.8127 (tp30) cc_final: 0.7637 (tt0) REVERT: B 443 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6767 (mt-10) REVERT: B 611 PHE cc_start: 0.6345 (m-10) cc_final: 0.6013 (m-10) REVERT: B 635 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8737 (mt-10) REVERT: B 669 MET cc_start: 0.9514 (OUTLIER) cc_final: 0.9303 (ptp) REVERT: A 31 GLU cc_start: 0.8132 (tp30) cc_final: 0.7754 (tp30) REVERT: A 36 LYS cc_start: 0.7384 (ttmt) cc_final: 0.6955 (mttm) REVERT: A 443 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6839 (mt-10) REVERT: A 592 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8290 (pt0) REVERT: A 622 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8607 (ttmt) outliers start: 51 outliers final: 24 residues processed: 196 average time/residue: 0.8135 time to fit residues: 171.6557 Evaluate side-chains 184 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 669 MET Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 563 LYS 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 83 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 12 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.096878 restraints weight = 19552.585| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.25 r_work: 0.2974 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0840 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= 0.135 Angle : 0.535 7.591 20246 Z= 0.301 Chirality : 0.044 0.139 2234 Planarity : 0.004 0.054 2296 Dihedral : 18.061 158.529 2532 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.42 % Favored : 92.45 % Rotamer: Outliers : 2.27 % Allowed : 36.05 % Favored : 61.69 % 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 aren not related in a simple way. whole: -0.39 (0.22), residues: 1536 helix: 0.69 (0.24), residues: 512 sheet: 0.92 (0.28), residues: 340 loop : -1.66 (0.24), residues: 684 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 0.029 0.001 PHE A 439 TRP 0.012 0.001 TRP A 222 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00303 (14792) covalent geometry : angle 0.53515 (20246) hydrogen bonds : bond 0.03721 ( 575) hydrogen bonds : angle 4.15069 ( 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 206 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7933 (mt-10) REVERT: B 371 GLU cc_start: 0.8218 (tp30) cc_final: 0.7722 (tt0) REVERT: B 440 ARG cc_start: 0.6247 (OUTLIER) cc_final: 0.5879 (tpt170) REVERT: B 443 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6907 (mt-10) REVERT: B 635 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8701 (mt-10) REVERT: A 31 GLU cc_start: 0.8079 (tp30) cc_final: 0.7823 (tp30) REVERT: A 36 LYS cc_start: 0.7334 (ttmt) cc_final: 0.6964 (mttm) REVERT: A 443 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6811 (mm-30) REVERT: A 458 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: A 622 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8450 (ttpt) outliers start: 32 outliers final: 15 residues processed: 197 average time/residue: 0.7352 time to fit residues: 157.0621 Evaluate side-chains 177 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 232 TYR 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 486 GLU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 622 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN A 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.093292 restraints weight = 19592.573| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.24 r_work: 0.2925 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 14792 Z= 0.247 Angle : 0.610 8.436 20246 Z= 0.338 Chirality : 0.047 0.147 2234 Planarity : 0.005 0.056 2296 Dihedral : 18.192 157.065 2532 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.94 % Favored : 91.93 % 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 aren not related in a simple way. whole: -0.51 (0.22), residues: 1536 helix: 0.69 (0.24), residues: 496 sheet: 0.71 (0.27), residues: 356 loop : -1.74 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 583 TYR 0.018 0.002 TYR B 743 PHE 0.033 0.002 PHE B 439 TRP 0.011 0.001 TRP B 222 HIS 0.003 0.001 HIS B 742 Details of bonding type rmsd covalent geometry : bond 0.00595 (14792) covalent geometry : angle 0.60962 (20246) hydrogen bonds : bond 0.04925 ( 575) hydrogen bonds : angle 4.34469 ( 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 226 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 166 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8579 (tt) REVERT: B 162 ASP cc_start: 0.7698 (t0) cc_final: 0.7433 (t0) REVERT: B 371 GLU cc_start: 0.8108 (tp30) cc_final: 0.7625 (tt0) REVERT: B 440 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.5939 (tpt170) REVERT: B 443 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6814 (mt-10) REVERT: B 622 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8597 (mtmt) REVERT: B 669 MET cc_start: 0.9492 (OUTLIER) cc_final: 0.9292 (ptp) REVERT: A 31 GLU cc_start: 0.8182 (tp30) cc_final: 0.7975 (tp30) REVERT: A 36 LYS cc_start: 0.7399 (ttmt) cc_final: 0.6938 (mttm) REVERT: A 443 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6864 (mt-10) REVERT: A 458 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8091 (mt-10) outliers start: 60 outliers final: 36 residues processed: 207 average time/residue: 0.7871 time to fit residues: 175.8900 Evaluate side-chains 203 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 669 MET Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 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 310 ASP Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 709 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: 3.9990 chunk 153 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3501 r_free = 0.3501 target = 0.127955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.096840 restraints weight = 19540.781| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.23 r_work: 0.2953 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14792 Z= 0.160 Angle : 0.558 7.395 20246 Z= 0.313 Chirality : 0.044 0.143 2234 Planarity : 0.004 0.056 2296 Dihedral : 18.100 157.962 2532 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.38 % Rotamer: Outliers : 4.32 % Allowed : 34.77 % Favored : 60.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.22), residues: 1536 helix: 0.69 (0.24), residues: 508 sheet: 0.88 (0.28), residues: 340 loop : -1.68 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 521 TYR 0.012 0.001 TYR B 743 PHE 0.030 0.001 PHE A 439 TRP 0.011 0.001 TRP A 222 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00371 (14792) covalent geometry : angle 0.55828 (20246) hydrogen bonds : bond 0.03971 ( 575) hydrogen bonds : angle 4.14341 ( 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 231 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 170 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8559 (tt) REVERT: B 204 ASP cc_start: 0.8351 (t0) cc_final: 0.8128 (t0) REVERT: B 371 GLU cc_start: 0.8160 (tp30) cc_final: 0.7682 (tt0) REVERT: B 440 ARG cc_start: 0.6211 (OUTLIER) cc_final: 0.5948 (tpt170) REVERT: B 443 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6908 (mt-10) REVERT: B 611 PHE cc_start: 0.6917 (m-10) cc_final: 0.6622 (m-10) REVERT: A 36 LYS cc_start: 0.7377 (ttmt) cc_final: 0.6912 (mttm) REVERT: A 443 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6784 (mt-10) REVERT: A 458 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8081 (mt-10) outliers start: 61 outliers final: 36 residues processed: 209 average time/residue: 0.7446 time to fit residues: 168.6389 Evaluate side-chains 198 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 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 407 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 616 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 44 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.094203 restraints weight = 19625.406| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.23 r_work: 0.2929 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14792 Z= 0.219 Angle : 0.601 7.641 20246 Z= 0.335 Chirality : 0.046 0.145 2234 Planarity : 0.005 0.066 2296 Dihedral : 18.146 157.214 2530 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.88 % Favored : 91.99 % Rotamer: Outliers : 4.82 % Allowed : 34.49 % 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 aren not related in a simple way. whole: -0.46 (0.22), residues: 1536 helix: 0.74 (0.24), residues: 496 sheet: 0.95 (0.28), residues: 350 loop : -1.83 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 521 TYR 0.016 0.001 TYR B 743 PHE 0.030 0.002 PHE A 439 TRP 0.012 0.001 TRP B 222 HIS 0.003 0.001 HIS A 742 Details of bonding type rmsd covalent geometry : bond 0.00523 (14792) covalent geometry : angle 0.60114 (20246) hydrogen bonds : bond 0.04576 ( 575) hydrogen bonds : angle 4.26397 ( 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 231 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 163 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8590 (tt) REVERT: B 162 ASP cc_start: 0.7701 (t0) cc_final: 0.7425 (t0) REVERT: B 204 ASP cc_start: 0.8408 (t0) cc_final: 0.8172 (t0) REVERT: B 371 GLU cc_start: 0.8106 (tp30) cc_final: 0.7627 (tt0) REVERT: B 440 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.5831 (tpp80) REVERT: B 443 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6813 (mt-10) REVERT: B 458 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: A 36 LYS cc_start: 0.7510 (ttmt) cc_final: 0.6898 (mttm) REVERT: A 443 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6848 (mt-10) REVERT: A 458 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: A 592 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8125 (pt0) REVERT: A 622 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8376 (ttpt) outliers start: 68 outliers final: 33 residues processed: 208 average time/residue: 0.7435 time to fit residues: 167.0696 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 : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 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 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 622 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: 6.9990 chunk 85 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 143 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.097812 restraints weight = 19345.499| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.21 r_work: 0.2977 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1083 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= 0.146 Angle : 0.555 8.409 20246 Z= 0.312 Chirality : 0.044 0.143 2234 Planarity : 0.005 0.061 2296 Dihedral : 18.077 157.664 2530 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.55 % Favored : 92.32 % Rotamer: Outliers : 3.82 % Allowed : 34.92 % 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 aren not related in a simple way. whole: -0.33 (0.22), residues: 1536 helix: 0.84 (0.24), residues: 500 sheet: 0.94 (0.28), residues: 344 loop : -1.67 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 521 TYR 0.012 0.001 TYR A 212 PHE 0.029 0.001 PHE A 439 TRP 0.011 0.001 TRP B 222 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00333 (14792) covalent geometry : angle 0.55547 (20246) hydrogen bonds : bond 0.03760 ( 575) hydrogen bonds : angle 4.08257 ( 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: 54 poor density : 169 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8538 (tt) REVERT: B 287 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7868 (tm-30) REVERT: B 371 GLU cc_start: 0.8223 (tp30) cc_final: 0.7753 (tt0) REVERT: B 440 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.5802 (tpp80) REVERT: B 443 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6899 (mt-10) REVERT: B 458 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: B 758 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7808 (tppp) REVERT: A 31 GLU cc_start: 0.8185 (tp30) cc_final: 0.7709 (tp30) REVERT: A 32 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8443 (mm-30) REVERT: A 36 LYS cc_start: 0.7486 (ttmt) cc_final: 0.6970 (mttm) REVERT: A 287 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 443 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6841 (mt-10) REVERT: A 458 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: A 592 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8070 (pt0) REVERT: A 622 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8387 (ttpt) REVERT: A 758 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7802 (tppp) outliers start: 54 outliers final: 29 residues processed: 208 average time/residue: 0.7322 time to fit residues: 165.7693 Evaluate side-chains 192 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 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 407 LEU Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 758 LYS Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 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 758 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: 6.9990 chunk 114 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN A 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.094183 restraints weight = 19302.699| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.27 r_work: 0.2934 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 14792 Z= 0.321 Angle : 0.687 8.337 20246 Z= 0.380 Chirality : 0.050 0.185 2234 Planarity : 0.005 0.057 2296 Dihedral : 18.326 156.678 2530 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.40 % Favored : 91.47 % Rotamer: Outliers : 3.82 % Allowed : 35.55 % Favored : 60.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.22), residues: 1536 helix: 0.41 (0.23), residues: 502 sheet: 0.85 (0.28), residues: 350 loop : -1.92 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 521 TYR 0.022 0.002 TYR A 743 PHE 0.036 0.002 PHE B 439 TRP 0.016 0.002 TRP B 222 HIS 0.004 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00778 (14792) covalent geometry : angle 0.68721 (20246) hydrogen bonds : bond 0.05636 ( 575) hydrogen bonds : angle 4.50227 ( 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 216 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8700 (tt) REVERT: B 162 ASP cc_start: 0.7987 (t0) cc_final: 0.7716 (t0) REVERT: B 371 GLU cc_start: 0.8199 (tp30) cc_final: 0.7768 (tt0) REVERT: B 440 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6160 (tpp80) REVERT: B 458 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: A 31 GLU cc_start: 0.8295 (tp30) cc_final: 0.7869 (tp30) REVERT: A 36 LYS cc_start: 0.7538 (ttmt) cc_final: 0.7037 (mttm) REVERT: A 443 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7004 (mt-10) REVERT: A 458 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: A 592 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8292 (pt0) REVERT: A 622 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8622 (ttpt) outliers start: 54 outliers final: 30 residues processed: 200 average time/residue: 0.7353 time to fit residues: 159.0413 Evaluate side-chains 187 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 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 395 ASP Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 519 ARG Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 608 VAL 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: 1.9990 chunk 143 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 93 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 ASN B 749 ASN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN A 749 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.129400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.098371 restraints weight = 19557.664| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.23 r_work: 0.2988 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1188 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= 0.131 Angle : 0.567 7.267 20246 Z= 0.320 Chirality : 0.044 0.187 2234 Planarity : 0.005 0.054 2296 Dihedral : 18.145 159.154 2530 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.03 % Favored : 92.84 % Rotamer: Outliers : 2.41 % Allowed : 37.04 % Favored : 60.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.22), residues: 1536 helix: 0.62 (0.24), residues: 512 sheet: 0.93 (0.28), residues: 344 loop : -1.71 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 521 TYR 0.015 0.001 TYR A 212 PHE 0.029 0.001 PHE A 439 TRP 0.012 0.001 TRP B 222 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00294 (14792) covalent geometry : angle 0.56682 (20246) hydrogen bonds : bond 0.03604 ( 575) hydrogen bonds : angle 4.04926 ( 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 195 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8587 (tt) REVERT: B 252 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6618 (mptt) REVERT: B 287 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 371 GLU cc_start: 0.8206 (tp30) cc_final: 0.7745 (tt0) REVERT: B 440 ARG cc_start: 0.6326 (OUTLIER) cc_final: 0.5688 (tpt170) REVERT: B 443 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6909 (mt-10) REVERT: B 458 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8063 (mm-30) REVERT: A 36 LYS cc_start: 0.7394 (ttmt) cc_final: 0.6944 (mttm) REVERT: A 157 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7946 (pt0) REVERT: A 287 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 443 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6869 (mt-10) REVERT: A 458 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8049 (mt-10) outliers start: 34 outliers final: 14 residues processed: 185 average time/residue: 0.7831 time to fit residues: 156.5225 Evaluate side-chains 168 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 770 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 48 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 140 optimal weight: 0.0170 overall best weight: 2.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.097901 restraints weight = 19388.644| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.20 r_work: 0.2976 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1220 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= 0.149 Angle : 0.577 7.095 20246 Z= 0.325 Chirality : 0.045 0.173 2234 Planarity : 0.005 0.054 2296 Dihedral : 18.073 157.614 2530 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.36 % Favored : 92.51 % Rotamer: Outliers : 1.63 % Allowed : 38.17 % Favored : 60.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.22), residues: 1536 helix: 1.00 (0.24), residues: 488 sheet: 0.79 (0.27), residues: 358 loop : -1.73 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 521 TYR 0.021 0.001 TYR B 214 PHE 0.029 0.001 PHE A 439 TRP 0.014 0.001 TRP B 222 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00342 (14792) covalent geometry : angle 0.57731 (20246) hydrogen bonds : bond 0.03780 ( 575) hydrogen bonds : angle 4.08109 ( 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 179 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8559 (tt) REVERT: B 252 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6633 (mptt) REVERT: B 287 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 358 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7904 (p) REVERT: B 371 GLU cc_start: 0.8165 (tp30) cc_final: 0.7681 (tt0) REVERT: B 443 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6853 (mt-10) REVERT: B 458 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: A 36 LYS cc_start: 0.7544 (ttmt) cc_final: 0.6964 (mttm) REVERT: A 157 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7982 (pt0) REVERT: A 287 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7836 (tm-30) REVERT: A 443 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6876 (mt-10) REVERT: A 458 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: A 583 ARG cc_start: 0.6839 (mmp80) cc_final: 0.6528 (mmp80) outliers start: 23 outliers final: 18 residues processed: 173 average time/residue: 0.7849 time to fit residues: 146.8375 Evaluate side-chains 176 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 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 156 TRP Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 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: 9.9990 chunk 154 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 133 optimal weight: 0.5980 chunk 125 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.094281 restraints weight = 19539.378| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.23 r_work: 0.2939 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14792 Z= 0.213 Angle : 0.618 8.104 20246 Z= 0.345 Chirality : 0.046 0.203 2234 Planarity : 0.005 0.054 2296 Dihedral : 18.129 156.682 2530 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.20 % Favored : 91.67 % Rotamer: Outliers : 2.05 % Allowed : 37.68 % Favored : 60.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.22), residues: 1536 helix: 0.81 (0.24), residues: 490 sheet: 1.00 (0.28), residues: 340 loop : -1.91 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 521 TYR 0.024 0.001 TYR B 214 PHE 0.029 0.002 PHE A 439 TRP 0.016 0.002 TRP A 222 HIS 0.003 0.001 HIS B 742 Details of bonding type rmsd covalent geometry : bond 0.00508 (14792) covalent geometry : angle 0.61769 (20246) hydrogen bonds : bond 0.04519 ( 575) hydrogen bonds : angle 4.26185 ( 1601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5220.25 seconds wall clock time: 89 minutes 37.38 seconds (5377.38 seconds total)