Starting phenix.real_space_refine on Tue Apr 7 05:06:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9olk_70595/04_2026/9olk_70595.cif Found real_map, /net/cci-nas-00/data/ceres_data/9olk_70595/04_2026/9olk_70595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9olk_70595/04_2026/9olk_70595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9olk_70595/04_2026/9olk_70595.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9olk_70595/04_2026/9olk_70595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9olk_70595/04_2026/9olk_70595.map" } resolution = 2.8 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= -0.001 sd= 0.048 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 132 5.16 5 C 16044 2.51 5 N 3892 2.21 5 O 4488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24568 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5997 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 5997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5997 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 5997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5997 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 5997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5997 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 190 Unusual residues: {'CPL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "B" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'CPL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'CPL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "D" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 100 Unusual residues: {'CPL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 5.28, per 1000 atoms: 0.21 Number of scatterers: 24568 At special positions: 0 Unit cell: (135, 135, 176.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 12 15.00 O 4488 8.00 N 3892 7.00 C 16044 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.0 seconds 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5696 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 0 sheets defined 78.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 51 through 62 Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 86 through 95 Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.671A pdb=" N LYS A 182 " --> pdb=" O MET A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 206 Processing helix chain 'A' and resid 208 through 222 Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.681A pdb=" N LEU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.895A pdb=" N ASN A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 276 removed outlier: 3.689A pdb=" N VAL A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 289 Processing helix chain 'A' and resid 306 through 316 Processing helix chain 'A' and resid 317 through 322 Processing helix chain 'A' and resid 323 through 335 removed outlier: 4.235A pdb=" N GLN A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 333 " --> pdb=" O GLN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.935A pdb=" N ARG A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 359 removed outlier: 4.004A pdb=" N LYS A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 370 removed outlier: 3.787A pdb=" N ALA A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 381 through 403 Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.604A pdb=" N ARG A 407 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 408 " --> pdb=" O SER A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 426 through 433 removed outlier: 3.736A pdb=" N LYS A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 459 removed outlier: 4.599A pdb=" N GLU A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 469 through 505 Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.696A pdb=" N PHE A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 550 removed outlier: 3.815A pdb=" N ILE A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.785A pdb=" N ALA A 554 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU A 557 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Proline residue: A 558 - end of helix Processing helix chain 'A' and resid 563 through 600 removed outlier: 3.579A pdb=" N PHE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 579 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 580 " --> pdb=" O ASP A 576 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU A 583 " --> pdb=" O LYS A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 624 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.662A pdb=" N SER A 633 " --> pdb=" O GLU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 676 removed outlier: 3.551A pdb=" N SER A 673 " --> pdb=" O MET A 669 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 676 " --> pdb=" O SER A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 694 removed outlier: 3.510A pdb=" N GLU A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.503A pdb=" N THR A 702 " --> pdb=" O ASP A 699 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A 703 " --> pdb=" O GLY A 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 699 through 703' Processing helix chain 'A' and resid 704 through 708 Processing helix chain 'A' and resid 773 through 795 removed outlier: 3.746A pdb=" N LYS A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 837 removed outlier: 3.904A pdb=" N LEU A 804 " --> pdb=" O ASN A 800 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 805 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 821 " --> pdb=" O GLU A 817 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 50 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 86 through 95 Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 114 through 123 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 136 through 144 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.671A pdb=" N LYS B 182 " --> pdb=" O MET B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 206 Processing helix chain 'B' and resid 208 through 222 Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.681A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.895A pdb=" N ASN B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 removed outlier: 3.689A pdb=" N VAL B 270 " --> pdb=" O CYS B 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 289 Processing helix chain 'B' and resid 306 through 316 Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 323 through 335 removed outlier: 4.235A pdb=" N GLN B 329 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 333 " --> pdb=" O GLN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.935A pdb=" N ARG B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 359 removed outlier: 4.003A pdb=" N LYS B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 370 removed outlier: 3.787A pdb=" N ALA B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 381 through 403 Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.604A pdb=" N ARG B 407 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 408 " --> pdb=" O SER B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 426 through 433 removed outlier: 3.737A pdb=" N LYS B 430 " --> pdb=" O ILE B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 459 removed outlier: 4.600A pdb=" N GLU B 455 " --> pdb=" O SER B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 466 Processing helix chain 'B' and resid 469 through 505 Processing helix chain 'B' and resid 516 through 522 removed outlier: 3.696A pdb=" N PHE B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 550 removed outlier: 3.815A pdb=" N ILE B 544 " --> pdb=" O GLY B 540 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 560 removed outlier: 3.785A pdb=" N ALA B 554 " --> pdb=" O SER B 551 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 557 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Proline residue: B 558 - end of helix Processing helix chain 'B' and resid 563 through 600 removed outlier: 3.579A pdb=" N PHE B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 579 " --> pdb=" O LYS B 575 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 580 " --> pdb=" O ASP B 576 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B 582 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU B 583 " --> pdb=" O LYS B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 624 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.662A pdb=" N SER B 633 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 676 removed outlier: 3.551A pdb=" N SER B 673 " --> pdb=" O MET B 669 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B 676 " --> pdb=" O SER B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 694 removed outlier: 3.510A pdb=" N GLU B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 703 removed outlier: 3.503A pdb=" N THR B 702 " --> pdb=" O ASP B 699 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU B 703 " --> pdb=" O GLY B 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 699 through 703' Processing helix chain 'B' and resid 704 through 708 Processing helix chain 'B' and resid 773 through 795 removed outlier: 3.745A pdb=" N LYS B 780 " --> pdb=" O GLN B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 837 removed outlier: 3.904A pdb=" N LEU B 804 " --> pdb=" O ASN B 800 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 805 " --> pdb=" O GLU B 801 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 806 " --> pdb=" O GLY B 802 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU B 820 " --> pdb=" O TYR B 816 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP B 821 " --> pdb=" O GLU B 817 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 51 through 62 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 86 through 95 Processing helix chain 'C' and resid 101 through 113 Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 136 through 144 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.671A pdb=" N LYS C 182 " --> pdb=" O MET C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 206 Processing helix chain 'C' and resid 208 through 222 Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.681A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 252 removed outlier: 3.895A pdb=" N ASN C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 276 removed outlier: 3.689A pdb=" N VAL C 270 " --> pdb=" O CYS C 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 289 Processing helix chain 'C' and resid 306 through 316 Processing helix chain 'C' and resid 317 through 322 Processing helix chain 'C' and resid 323 through 335 removed outlier: 4.235A pdb=" N GLN C 329 " --> pdb=" O ASN C 325 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 332 " --> pdb=" O GLN C 328 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 333 " --> pdb=" O GLN C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.935A pdb=" N ARG C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 359 removed outlier: 4.003A pdb=" N LYS C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 351 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 358 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 370 removed outlier: 3.787A pdb=" N ALA C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 381 through 403 Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.603A pdb=" N ARG C 407 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE C 408 " --> pdb=" O SER C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 426 through 433 removed outlier: 3.735A pdb=" N LYS C 430 " --> pdb=" O ILE C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 459 removed outlier: 4.599A pdb=" N GLU C 455 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 469 through 505 Processing helix chain 'C' and resid 516 through 522 removed outlier: 3.695A pdb=" N PHE C 522 " --> pdb=" O GLU C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 550 removed outlier: 3.815A pdb=" N ILE C 544 " --> pdb=" O GLY C 540 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE C 550 " --> pdb=" O VAL C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 560 removed outlier: 3.785A pdb=" N ALA C 554 " --> pdb=" O SER C 551 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU C 557 " --> pdb=" O ALA C 554 " (cutoff:3.500A) Proline residue: C 558 - end of helix Processing helix chain 'C' and resid 563 through 600 removed outlier: 3.579A pdb=" N PHE C 578 " --> pdb=" O VAL C 574 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 579 " --> pdb=" O LYS C 575 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 582 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU C 583 " --> pdb=" O LYS C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 624 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.662A pdb=" N SER C 633 " --> pdb=" O GLU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 676 removed outlier: 3.551A pdb=" N SER C 673 " --> pdb=" O MET C 669 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU C 676 " --> pdb=" O SER C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 694 removed outlier: 3.510A pdb=" N GLU C 684 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 703 removed outlier: 3.503A pdb=" N THR C 702 " --> pdb=" O ASP C 699 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU C 703 " --> pdb=" O GLY C 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 699 through 703' Processing helix chain 'C' and resid 704 through 708 Processing helix chain 'C' and resid 773 through 795 removed outlier: 3.746A pdb=" N LYS C 780 " --> pdb=" O GLN C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 837 removed outlier: 3.904A pdb=" N LEU C 804 " --> pdb=" O ASN C 800 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 805 " --> pdb=" O GLU C 801 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU C 806 " --> pdb=" O GLY C 802 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU C 820 " --> pdb=" O TYR C 816 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP C 821 " --> pdb=" O GLU C 817 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS C 834 " --> pdb=" O ALA C 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 50 Processing helix chain 'D' and resid 51 through 62 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 86 through 95 Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 114 through 123 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 136 through 144 Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 172 through 182 removed outlier: 3.671A pdb=" N LYS D 182 " --> pdb=" O MET D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 206 Processing helix chain 'D' and resid 208 through 222 Processing helix chain 'D' and resid 223 through 231 removed outlier: 3.681A pdb=" N LEU D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.894A pdb=" N ASN D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 276 removed outlier: 3.689A pdb=" N VAL D 270 " --> pdb=" O CYS D 266 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 289 Processing helix chain 'D' and resid 306 through 316 Processing helix chain 'D' and resid 317 through 322 Processing helix chain 'D' and resid 323 through 335 removed outlier: 4.235A pdb=" N GLN D 329 " --> pdb=" O ASN D 325 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 332 " --> pdb=" O GLN D 328 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE D 333 " --> pdb=" O GLN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 removed outlier: 3.935A pdb=" N ARG D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 359 removed outlier: 4.003A pdb=" N LYS D 349 " --> pdb=" O THR D 345 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 370 removed outlier: 3.787A pdb=" N ALA D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 381 through 403 Processing helix chain 'D' and resid 404 through 408 removed outlier: 3.604A pdb=" N ARG D 407 " --> pdb=" O ALA D 404 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE D 408 " --> pdb=" O SER D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 404 through 408' Processing helix chain 'D' and resid 426 through 433 removed outlier: 3.736A pdb=" N LYS D 430 " --> pdb=" O ILE D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 459 removed outlier: 4.599A pdb=" N GLU D 455 " --> pdb=" O SER D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 466 Processing helix chain 'D' and resid 469 through 505 Processing helix chain 'D' and resid 516 through 522 removed outlier: 3.696A pdb=" N PHE D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 550 removed outlier: 3.815A pdb=" N ILE D 544 " --> pdb=" O GLY D 540 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE D 550 " --> pdb=" O VAL D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 560 removed outlier: 3.785A pdb=" N ALA D 554 " --> pdb=" O SER D 551 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU D 557 " --> pdb=" O ALA D 554 " (cutoff:3.500A) Proline residue: D 558 - end of helix Processing helix chain 'D' and resid 563 through 600 removed outlier: 3.579A pdb=" N PHE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS D 579 " --> pdb=" O LYS D 575 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 580 " --> pdb=" O ASP D 576 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL D 582 " --> pdb=" O PHE D 578 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU D 583 " --> pdb=" O LYS D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 624 Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.663A pdb=" N SER D 633 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 676 removed outlier: 3.552A pdb=" N SER D 673 " --> pdb=" O MET D 669 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU D 676 " --> pdb=" O SER D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 694 removed outlier: 3.510A pdb=" N GLU D 684 " --> pdb=" O ASP D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 703 removed outlier: 3.503A pdb=" N THR D 702 " --> pdb=" O ASP D 699 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU D 703 " --> pdb=" O GLY D 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 699 through 703' Processing helix chain 'D' and resid 704 through 708 Processing helix chain 'D' and resid 773 through 795 removed outlier: 3.746A pdb=" N LYS D 780 " --> pdb=" O GLN D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 837 removed outlier: 3.904A pdb=" N LEU D 804 " --> pdb=" O ASN D 800 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS D 805 " --> pdb=" O GLU D 801 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU D 806 " --> pdb=" O GLY D 802 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU D 820 " --> pdb=" O TYR D 816 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP D 821 " --> pdb=" O GLU D 817 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER D 823 " --> pdb=" O LEU D 819 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS D 834 " --> pdb=" O ALA D 830 " (cutoff:3.500A) 1516 hydrogen bonds defined for protein. 4476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3964 1.30 - 1.43: 6469 1.43 - 1.56: 14411 1.56 - 1.69: 24 1.69 - 1.82: 216 Bond restraints: 25084 Sorted by residual: bond pdb=" C11 CPL C 903 " pdb=" O3 CPL C 903 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C11 CPL A 904 " pdb=" O3 CPL A 904 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C11 CPL A 902 " pdb=" O3 CPL A 902 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C11 CPL B 903 " pdb=" O3 CPL B 903 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C11 CPL A 901 " pdb=" O3 CPL A 901 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.88e+01 ... (remaining 25079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.91: 33383 4.91 - 9.82: 421 9.82 - 14.73: 36 14.73 - 19.64: 4 19.64 - 24.56: 12 Bond angle restraints: 33856 Sorted by residual: angle pdb=" C5 CPL B 901 " pdb=" N CPL B 901 " pdb=" C8 CPL B 901 " ideal model delta sigma weight residual 112.02 87.46 24.56 3.00e+00 1.11e-01 6.70e+01 angle pdb=" C5 CPL A 901 " pdb=" N CPL A 901 " pdb=" C8 CPL A 901 " ideal model delta sigma weight residual 112.02 87.47 24.55 3.00e+00 1.11e-01 6.70e+01 angle pdb=" C5 CPL D 901 " pdb=" N CPL D 901 " pdb=" C8 CPL D 901 " ideal model delta sigma weight residual 112.02 87.50 24.52 3.00e+00 1.11e-01 6.68e+01 angle pdb=" C5 CPL C 901 " pdb=" N CPL C 901 " pdb=" C8 CPL C 901 " ideal model delta sigma weight residual 112.02 87.50 24.52 3.00e+00 1.11e-01 6.68e+01 angle pdb=" CA PHE B 383 " pdb=" C PHE B 383 " pdb=" O PHE B 383 " ideal model delta sigma weight residual 120.55 112.27 8.28 1.06e+00 8.90e-01 6.10e+01 ... (remaining 33851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 14500 35.12 - 70.24: 616 70.24 - 105.36: 72 105.36 - 140.47: 12 140.47 - 175.59: 4 Dihedral angle restraints: 15204 sinusoidal: 6412 harmonic: 8792 Sorted by residual: dihedral pdb=" CD ARG D 374 " pdb=" NE ARG D 374 " pdb=" CZ ARG D 374 " pdb=" NH1 ARG D 374 " ideal model delta sinusoidal sigma weight residual 0.00 -85.22 85.22 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CD ARG A 374 " pdb=" NE ARG A 374 " pdb=" CZ ARG A 374 " pdb=" NH1 ARG A 374 " ideal model delta sinusoidal sigma weight residual 0.00 -85.21 85.21 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CD ARG B 374 " pdb=" NE ARG B 374 " pdb=" CZ ARG B 374 " pdb=" NH1 ARG B 374 " ideal model delta sinusoidal sigma weight residual 0.00 -85.21 85.21 1 1.00e+01 1.00e-02 8.80e+01 ... (remaining 15201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2677 0.072 - 0.145: 796 0.145 - 0.217: 251 0.217 - 0.290: 32 0.290 - 0.362: 12 Chirality restraints: 3768 Sorted by residual: chirality pdb=" C2 CPL A 902 " pdb=" C1 CPL A 902 " pdb=" C3 CPL A 902 " pdb=" O2 CPL A 902 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C2 CPL C 903 " pdb=" C1 CPL C 903 " pdb=" C3 CPL C 903 " pdb=" O2 CPL C 903 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C2 CPL B 903 " pdb=" C1 CPL B 903 " pdb=" C3 CPL B 903 " pdb=" O2 CPL B 903 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 3765 not shown) Planarity restraints: 4224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 374 " -1.104 9.50e-02 1.11e+02 4.95e-01 1.48e+02 pdb=" NE ARG C 374 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG C 374 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 374 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG C 374 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 374 " 1.103 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG B 374 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 374 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 374 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 374 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 374 " 1.103 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG A 374 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 374 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 374 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 374 " 0.017 2.00e-02 2.50e+03 ... (remaining 4221 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6543 2.82 - 3.34: 23508 3.34 - 3.86: 38173 3.86 - 4.38: 46019 4.38 - 4.90: 77160 Nonbonded interactions: 191403 Sorted by model distance: nonbonded pdb=" O LEU A 692 " pdb=" OG SER A 695 " model vdw 2.300 3.040 nonbonded pdb=" O LEU B 692 " pdb=" OG SER B 695 " model vdw 2.300 3.040 nonbonded pdb=" O LEU D 692 " pdb=" OG SER D 695 " model vdw 2.300 3.040 nonbonded pdb=" O LEU C 692 " pdb=" OG SER C 695 " model vdw 2.301 3.040 nonbonded pdb=" OD2 ASP A 206 " pdb=" OG SER A 209 " model vdw 2.319 3.040 ... (remaining 191398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 901 or (resid 902 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C4 or name C40 or name C41 or name C42 or name C43 or name C44 or name C45 or na \ me C5 or name C6 or name C7 or name C8 or name O11 or name O1P or name O2 or nam \ e O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 23 through 901 or (resid 902 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C4 or name C40 or name C41 or name C42 or name C43 or name C44 or name C45 or na \ me C5 or name C6 or name C7 or name C8 or name O11 or name O1P or name O2 or nam \ e O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'C' and (resid 23 through 901 or (resid 902 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C4 or name C40 or name C41 or name C42 or name C43 or name C44 or name C45 or na \ me C5 or name C6 or name C7 or name C8 or name O11 or name O1P or name O2 or nam \ e O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'D' and (resid 23 through 901 or (resid 902 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C4 or name C40 or name C41 or name C42 or name C43 or name C44 or name C45 or na \ me C5 or name C6 or name C7 or name C8 or name O11 or name O1P or name O2 or nam \ e O2P or name O3 or name O31 or name O3P or name O4P or name P )))) } 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.960 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 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 : 0.011 0.134 25088 Z= 0.785 Angle : 1.621 24.555 33856 Z= 1.081 Chirality : 0.077 0.362 3768 Planarity : 0.036 0.495 4224 Dihedral : 18.865 175.594 9508 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.82 % Favored : 93.64 % Rotamer: Outliers : 1.07 % Allowed : 10.73 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.14), residues: 2956 helix: -1.13 (0.10), residues: 2080 sheet: None (None), residues: 0 loop : -2.34 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 204 TYR 0.013 0.002 TYR D 648 PHE 0.026 0.002 PHE D 393 TRP 0.019 0.003 TRP C 334 HIS 0.005 0.001 HIS B 834 Details of bonding type rmsd covalent geometry : bond 0.01101 (25084) covalent geometry : angle 1.62107 (33856) hydrogen bonds : bond 0.22707 ( 1516) hydrogen bonds : angle 7.35168 ( 4476) Misc. bond : bond 0.13169 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 395 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7615 (tttt) cc_final: 0.7237 (ttmt) REVERT: A 188 ARG cc_start: 0.6752 (mtm-85) cc_final: 0.6400 (mtp85) REVERT: A 200 MET cc_start: 0.7249 (mtp) cc_final: 0.6461 (mmm) REVERT: A 409 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6842 (mm-30) REVERT: A 469 TRP cc_start: 0.5443 (OUTLIER) cc_final: 0.4352 (m100) REVERT: A 578 PHE cc_start: 0.7500 (t80) cc_final: 0.6812 (m-10) REVERT: A 630 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8186 (mt-10) REVERT: A 671 ASN cc_start: 0.6984 (m-40) cc_final: 0.6759 (m110) REVERT: B 57 LYS cc_start: 0.7621 (tttt) cc_final: 0.7216 (ttmt) REVERT: B 188 ARG cc_start: 0.6753 (mtm-85) cc_final: 0.6365 (mtp85) REVERT: B 200 MET cc_start: 0.7253 (mtp) cc_final: 0.6464 (mmm) REVERT: B 409 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6775 (mm-30) REVERT: B 469 TRP cc_start: 0.5441 (OUTLIER) cc_final: 0.4360 (m100) REVERT: B 578 PHE cc_start: 0.7504 (t80) cc_final: 0.6815 (m-10) REVERT: B 630 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 671 ASN cc_start: 0.6960 (m-40) cc_final: 0.6738 (m110) REVERT: C 57 LYS cc_start: 0.7645 (tttt) cc_final: 0.7262 (ttmt) REVERT: C 171 GLN cc_start: 0.8201 (mt0) cc_final: 0.7870 (mm-40) REVERT: C 188 ARG cc_start: 0.6716 (mtm-85) cc_final: 0.6345 (mtp85) REVERT: C 200 MET cc_start: 0.7258 (mtp) cc_final: 0.6449 (mmm) REVERT: C 409 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6848 (mm-30) REVERT: C 469 TRP cc_start: 0.5448 (OUTLIER) cc_final: 0.4383 (m100) REVERT: C 578 PHE cc_start: 0.7524 (t80) cc_final: 0.6819 (m-10) REVERT: C 630 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8214 (mt-10) REVERT: C 671 ASN cc_start: 0.6851 (m-40) cc_final: 0.6639 (m110) REVERT: D 57 LYS cc_start: 0.7641 (tttt) cc_final: 0.7260 (ttmt) REVERT: D 162 THR cc_start: 0.7736 (p) cc_final: 0.7032 (t) REVERT: D 171 GLN cc_start: 0.8218 (mt0) cc_final: 0.7932 (mm-40) REVERT: D 188 ARG cc_start: 0.6735 (mtm-85) cc_final: 0.6372 (mtp85) REVERT: D 200 MET cc_start: 0.7246 (mtp) cc_final: 0.6409 (mmm) REVERT: D 409 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6828 (mm-30) REVERT: D 469 TRP cc_start: 0.5425 (OUTLIER) cc_final: 0.4350 (m100) REVERT: D 578 PHE cc_start: 0.7511 (t80) cc_final: 0.6813 (m-10) REVERT: D 630 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8179 (mt-10) REVERT: D 671 ASN cc_start: 0.6941 (m-40) cc_final: 0.6702 (m110) outliers start: 28 outliers final: 0 residues processed: 415 average time/residue: 0.7070 time to fit residues: 331.8070 Evaluate side-chains 319 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 315 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 TRP Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain C residue 469 TRP Chi-restraints excluded: chain D residue 469 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.0270 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.2980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 327 GLN A 664 ASN A 796 ASN B 79 GLN B 664 ASN C 79 GLN C 664 ASN D 79 GLN D 664 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.229381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.180923 restraints weight = 26007.728| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.08 r_work: 0.3844 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25088 Z= 0.156 Angle : 0.593 6.946 33856 Z= 0.308 Chirality : 0.040 0.133 3768 Planarity : 0.005 0.062 4224 Dihedral : 16.378 165.952 3700 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.94 % Favored : 96.92 % Rotamer: Outliers : 4.07 % Allowed : 13.93 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 2956 helix: 1.07 (0.11), residues: 2132 sheet: None (None), residues: 0 loop : -1.45 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 462 TYR 0.017 0.001 TYR D 192 PHE 0.012 0.001 PHE A 622 TRP 0.010 0.001 TRP D 444 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00288 (25084) covalent geometry : angle 0.59340 (33856) hydrogen bonds : bond 0.07603 ( 1516) hydrogen bonds : angle 4.34622 ( 4476) Misc. bond : bond 0.00136 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 329 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: A 57 LYS cc_start: 0.7795 (tttt) cc_final: 0.7391 (ttmt) REVERT: A 60 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6345 (mp0) REVERT: A 61 GLU cc_start: 0.6700 (mm-30) cc_final: 0.6482 (mm-30) REVERT: A 200 MET cc_start: 0.7050 (mtp) cc_final: 0.6354 (mmm) REVERT: A 409 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7258 (mm-30) REVERT: A 438 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5980 (mp0) REVERT: A 578 PHE cc_start: 0.7423 (t80) cc_final: 0.6654 (m-10) REVERT: A 579 LYS cc_start: 0.7656 (ttmm) cc_final: 0.7032 (ttpp) REVERT: A 630 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8259 (mt-10) REVERT: A 684 GLU cc_start: 0.7286 (tp30) cc_final: 0.7071 (mm-30) REVERT: A 801 GLU cc_start: 0.7853 (pt0) cc_final: 0.7640 (mt-10) REVERT: B 48 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: B 57 LYS cc_start: 0.7760 (tttt) cc_final: 0.7359 (ttmt) REVERT: B 60 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: B 61 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6538 (mm-30) REVERT: B 200 MET cc_start: 0.6984 (mtp) cc_final: 0.6313 (mmm) REVERT: B 409 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7270 (mm-30) REVERT: B 438 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.6026 (mp0) REVERT: B 578 PHE cc_start: 0.7463 (t80) cc_final: 0.6656 (m-10) REVERT: B 579 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7049 (ttpp) REVERT: B 630 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8259 (mt-10) REVERT: C 48 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: C 57 LYS cc_start: 0.7799 (tttt) cc_final: 0.7391 (ttmt) REVERT: C 60 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: C 61 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6508 (mm-30) REVERT: C 200 MET cc_start: 0.7029 (mtp) cc_final: 0.6320 (mmm) REVERT: C 409 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7269 (mm-30) REVERT: C 438 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5905 (mp0) REVERT: C 578 PHE cc_start: 0.7385 (t80) cc_final: 0.6669 (m-10) REVERT: C 579 LYS cc_start: 0.7661 (ttmm) cc_final: 0.7036 (ttpp) REVERT: C 630 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8328 (mt-10) REVERT: C 801 GLU cc_start: 0.7854 (pt0) cc_final: 0.7650 (mt-10) REVERT: D 48 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: D 57 LYS cc_start: 0.7802 (tttt) cc_final: 0.7391 (ttmt) REVERT: D 60 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6320 (mp0) REVERT: D 61 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6474 (mm-30) REVERT: D 200 MET cc_start: 0.7038 (mtp) cc_final: 0.6313 (mmm) REVERT: D 409 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7280 (mm-30) REVERT: D 438 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5981 (mp0) REVERT: D 578 PHE cc_start: 0.7430 (t80) cc_final: 0.6647 (m-10) REVERT: D 630 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8273 (mt-10) REVERT: D 801 GLU cc_start: 0.7856 (pt0) cc_final: 0.7634 (mt-10) outliers start: 107 outliers final: 38 residues processed: 390 average time/residue: 0.6672 time to fit residues: 298.5738 Evaluate side-chains 346 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 296 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 670 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 177 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 chunk 64 optimal weight: 20.0000 chunk 163 optimal weight: 0.9990 chunk 208 optimal weight: 0.6980 chunk 265 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN B 498 GLN C 498 GLN D 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.229950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.171818 restraints weight = 25964.740| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.01 r_work: 0.3840 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25088 Z= 0.130 Angle : 0.500 6.088 33856 Z= 0.262 Chirality : 0.038 0.159 3768 Planarity : 0.004 0.036 4224 Dihedral : 15.160 172.251 3692 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.19 % Favored : 95.67 % Rotamer: Outliers : 2.97 % Allowed : 16.40 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.16), residues: 2956 helix: 1.87 (0.11), residues: 2128 sheet: None (None), residues: 0 loop : -1.18 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 380 TYR 0.015 0.001 TYR A 150 PHE 0.010 0.001 PHE A 642 TRP 0.011 0.001 TRP A 444 HIS 0.004 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00242 (25084) covalent geometry : angle 0.50036 (33856) hydrogen bonds : bond 0.06148 ( 1516) hydrogen bonds : angle 3.83236 ( 4476) Misc. bond : bond 0.00042 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 306 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: A 57 LYS cc_start: 0.7734 (tttt) cc_final: 0.7314 (ttmt) REVERT: A 60 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6205 (mp0) REVERT: A 162 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7041 (t) REVERT: A 200 MET cc_start: 0.7057 (mtp) cc_final: 0.6355 (mmm) REVERT: A 409 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7263 (mm-30) REVERT: A 530 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7139 (mp) REVERT: A 557 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6877 (mp) REVERT: A 578 PHE cc_start: 0.7478 (t80) cc_final: 0.6560 (m-10) REVERT: A 579 LYS cc_start: 0.7586 (ttmm) cc_final: 0.7312 (ttmp) REVERT: A 630 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8241 (mt-10) REVERT: B 48 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: B 57 LYS cc_start: 0.7741 (tttt) cc_final: 0.7319 (ttmt) REVERT: B 60 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6145 (mp0) REVERT: B 150 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8364 (p90) REVERT: B 162 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7038 (t) REVERT: B 200 MET cc_start: 0.7065 (mtp) cc_final: 0.6354 (mmm) REVERT: B 409 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7260 (mm-30) REVERT: B 530 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7106 (mp) REVERT: B 557 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6964 (mp) REVERT: B 578 PHE cc_start: 0.7361 (t80) cc_final: 0.6560 (m-10) REVERT: B 579 LYS cc_start: 0.7590 (ttmm) cc_final: 0.7320 (ttmp) REVERT: B 630 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8246 (mt-10) REVERT: B 821 ASP cc_start: 0.6371 (m-30) cc_final: 0.6161 (m-30) REVERT: C 48 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: C 57 LYS cc_start: 0.7718 (tttt) cc_final: 0.7294 (ttmt) REVERT: C 60 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6095 (mp0) REVERT: C 150 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8391 (p90) REVERT: C 162 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7019 (t) REVERT: C 200 MET cc_start: 0.7071 (mtp) cc_final: 0.6354 (mmm) REVERT: C 409 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7269 (mm-30) REVERT: C 530 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7115 (mp) REVERT: C 557 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6949 (mp) REVERT: C 578 PHE cc_start: 0.7253 (t80) cc_final: 0.6544 (m-10) REVERT: C 579 LYS cc_start: 0.7555 (ttmm) cc_final: 0.7272 (ttmp) REVERT: C 821 ASP cc_start: 0.6292 (m-30) cc_final: 0.6091 (m-30) REVERT: D 48 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: D 57 LYS cc_start: 0.7741 (tttt) cc_final: 0.7318 (ttmt) REVERT: D 60 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: D 162 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7016 (t) REVERT: D 200 MET cc_start: 0.7078 (mtp) cc_final: 0.6347 (mmm) REVERT: D 409 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7286 (mm-30) REVERT: D 530 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7135 (mp) REVERT: D 557 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6982 (mp) REVERT: D 578 PHE cc_start: 0.7237 (t80) cc_final: 0.6536 (m-10) REVERT: D 579 LYS cc_start: 0.7545 (ttmm) cc_final: 0.7249 (ttmp) outliers start: 78 outliers final: 31 residues processed: 360 average time/residue: 0.6226 time to fit residues: 258.6804 Evaluate side-chains 345 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 292 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 670 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 282 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 281 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 287 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 809 GLN B 327 GLN B 809 GLN C 327 GLN C 809 GLN D 327 GLN D 809 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.219037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.172917 restraints weight = 25751.883| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.94 r_work: 0.3625 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 25088 Z= 0.260 Angle : 0.678 9.939 33856 Z= 0.352 Chirality : 0.044 0.146 3768 Planarity : 0.005 0.043 4224 Dihedral : 15.314 179.776 3692 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.80 % Favored : 95.06 % Rotamer: Outliers : 4.38 % Allowed : 16.02 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.15), residues: 2956 helix: 1.41 (0.11), residues: 2120 sheet: None (None), residues: 0 loop : -1.37 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 785 TYR 0.026 0.002 TYR D 150 PHE 0.014 0.002 PHE D 588 TRP 0.018 0.002 TRP D 444 HIS 0.009 0.002 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00626 (25084) covalent geometry : angle 0.67804 (33856) hydrogen bonds : bond 0.09035 ( 1516) hydrogen bonds : angle 4.11046 ( 4476) Misc. bond : bond 0.00064 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 297 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: A 57 LYS cc_start: 0.7963 (tttt) cc_final: 0.7545 (ttmt) REVERT: A 60 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6337 (mp0) REVERT: A 162 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.8003 (p) REVERT: A 200 MET cc_start: 0.7102 (mtp) cc_final: 0.6501 (mmm) REVERT: A 409 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7346 (mm-30) REVERT: A 530 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7249 (mp) REVERT: A 557 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7163 (mp) REVERT: A 576 ASP cc_start: 0.6503 (m-30) cc_final: 0.5985 (t0) REVERT: A 578 PHE cc_start: 0.7586 (t80) cc_final: 0.6796 (m-10) REVERT: A 579 LYS cc_start: 0.7809 (ttmm) cc_final: 0.7545 (ttmp) REVERT: B 48 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: B 57 LYS cc_start: 0.7909 (tttt) cc_final: 0.7497 (ttmt) REVERT: B 60 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: B 162 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.8003 (p) REVERT: B 200 MET cc_start: 0.7092 (mtp) cc_final: 0.6492 (mmm) REVERT: B 409 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7340 (mm-30) REVERT: B 530 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7264 (mp) REVERT: B 557 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7141 (mp) REVERT: B 576 ASP cc_start: 0.6611 (m-30) cc_final: 0.6057 (t0) REVERT: B 578 PHE cc_start: 0.7612 (t80) cc_final: 0.6817 (m-10) REVERT: B 579 LYS cc_start: 0.7777 (ttmm) cc_final: 0.7506 (ttmp) REVERT: C 48 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: C 57 LYS cc_start: 0.7941 (tttt) cc_final: 0.7525 (ttmt) REVERT: C 60 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: C 162 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8042 (p) REVERT: C 200 MET cc_start: 0.7136 (mtp) cc_final: 0.6530 (mmm) REVERT: C 409 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7333 (mm-30) REVERT: C 518 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6186 (mp0) REVERT: C 530 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7203 (mp) REVERT: C 576 ASP cc_start: 0.6571 (m-30) cc_final: 0.6159 (t0) REVERT: C 578 PHE cc_start: 0.7528 (t80) cc_final: 0.6847 (m-10) REVERT: C 579 LYS cc_start: 0.7758 (ttmm) cc_final: 0.7479 (ttmp) REVERT: D 48 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: D 57 LYS cc_start: 0.7957 (tttt) cc_final: 0.7541 (ttmt) REVERT: D 60 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: D 73 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8540 (mmp) REVERT: D 162 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7997 (p) REVERT: D 200 MET cc_start: 0.7154 (mtp) cc_final: 0.6534 (mmm) REVERT: D 409 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7358 (mm-30) REVERT: D 438 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.6053 (mp0) REVERT: D 518 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6161 (mp0) REVERT: D 530 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7204 (mp) REVERT: D 576 ASP cc_start: 0.6508 (m-30) cc_final: 0.6010 (t0) REVERT: D 578 PHE cc_start: 0.7493 (t80) cc_final: 0.6828 (m-10) REVERT: D 579 LYS cc_start: 0.7790 (ttmm) cc_final: 0.7463 (ttmp) outliers start: 115 outliers final: 57 residues processed: 382 average time/residue: 0.6670 time to fit residues: 291.1438 Evaluate side-chains 359 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 282 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 670 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 246 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 275 optimal weight: 6.9990 chunk 151 optimal weight: 0.2980 chunk 245 optimal weight: 0.8980 chunk 272 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN A 776 GLN A 809 GLN B 498 GLN B 809 GLN C 809 GLN D 493 GLN D 498 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.223975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.164901 restraints weight = 25715.549| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.00 r_work: 0.3761 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 25088 Z= 0.138 Angle : 0.513 6.294 33856 Z= 0.270 Chirality : 0.039 0.132 3768 Planarity : 0.004 0.041 4224 Dihedral : 14.681 169.120 3692 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.61 % Allowed : 16.82 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.15), residues: 2956 helix: 1.82 (0.11), residues: 2124 sheet: None (None), residues: 0 loop : -1.17 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 374 TYR 0.018 0.001 TYR A 150 PHE 0.009 0.001 PHE C 393 TRP 0.008 0.001 TRP A 685 HIS 0.004 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00281 (25084) covalent geometry : angle 0.51270 (33856) hydrogen bonds : bond 0.06526 ( 1516) hydrogen bonds : angle 3.81389 ( 4476) Misc. bond : bond 0.00005 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 285 time to evaluate : 0.946 Fit side-chains REVERT: A 48 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: A 57 LYS cc_start: 0.7789 (tttt) cc_final: 0.7411 (ttmt) REVERT: A 60 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6291 (mp0) REVERT: A 91 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: A 200 MET cc_start: 0.6967 (mtp) cc_final: 0.6338 (mmm) REVERT: A 380 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.5664 (mpp80) REVERT: A 409 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7336 (mm-30) REVERT: A 430 LYS cc_start: 0.7323 (tppt) cc_final: 0.6908 (mmtp) REVERT: A 439 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6630 (mpp) REVERT: A 576 ASP cc_start: 0.6389 (m-30) cc_final: 0.6020 (t0) REVERT: A 578 PHE cc_start: 0.7679 (t80) cc_final: 0.6784 (m-10) REVERT: A 579 LYS cc_start: 0.7665 (ttmm) cc_final: 0.7305 (ttmp) REVERT: A 805 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7572 (tttm) REVERT: B 48 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: B 57 LYS cc_start: 0.7824 (tttt) cc_final: 0.7440 (ttmt) REVERT: B 60 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: B 200 MET cc_start: 0.6976 (mtp) cc_final: 0.6349 (mmm) REVERT: B 380 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.5632 (mpp80) REVERT: B 409 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7329 (mm-30) REVERT: B 430 LYS cc_start: 0.7320 (tppt) cc_final: 0.6901 (mmtp) REVERT: B 439 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6640 (mpp) REVERT: B 576 ASP cc_start: 0.6405 (m-30) cc_final: 0.6032 (t0) REVERT: B 578 PHE cc_start: 0.7689 (t80) cc_final: 0.6797 (m-10) REVERT: B 579 LYS cc_start: 0.7682 (ttmm) cc_final: 0.7387 (ttmp) REVERT: B 805 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7585 (tttm) REVERT: C 48 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: C 57 LYS cc_start: 0.7832 (tttt) cc_final: 0.7446 (ttmt) REVERT: C 60 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6132 (mp0) REVERT: C 200 MET cc_start: 0.6911 (mtp) cc_final: 0.6341 (mmm) REVERT: C 380 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.5654 (mpp80) REVERT: C 409 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7313 (mm-30) REVERT: C 439 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6598 (mpp) REVERT: C 576 ASP cc_start: 0.6374 (m-30) cc_final: 0.6025 (t0) REVERT: C 578 PHE cc_start: 0.7671 (t80) cc_final: 0.6786 (m-10) REVERT: C 579 LYS cc_start: 0.7685 (ttmm) cc_final: 0.7312 (ttmp) REVERT: D 48 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: D 57 LYS cc_start: 0.7794 (tttt) cc_final: 0.7417 (ttmt) REVERT: D 60 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: D 73 MET cc_start: 0.8713 (tpt) cc_final: 0.8432 (mmp) REVERT: D 200 MET cc_start: 0.6917 (mtp) cc_final: 0.6345 (mmm) REVERT: D 380 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.5523 (mpp80) REVERT: D 409 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7320 (mm-30) REVERT: D 430 LYS cc_start: 0.7321 (tppt) cc_final: 0.6916 (mmtp) REVERT: D 439 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6617 (mpp) REVERT: D 576 ASP cc_start: 0.6338 (m-30) cc_final: 0.6013 (t0) REVERT: D 578 PHE cc_start: 0.7683 (t80) cc_final: 0.6796 (m-10) REVERT: D 579 LYS cc_start: 0.7673 (ttmm) cc_final: 0.7299 (ttmp) outliers start: 95 outliers final: 35 residues processed: 350 average time/residue: 0.6706 time to fit residues: 268.3048 Evaluate side-chains 334 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 280 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 805 LYS Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 805 LYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 380 ARG Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 799 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 203 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 80 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 809 GLN B 809 GLN D 776 GLN ** D 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.223152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.164248 restraints weight = 25732.593| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.23 r_work: 0.3728 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25088 Z= 0.149 Angle : 0.530 6.919 33856 Z= 0.276 Chirality : 0.039 0.123 3768 Planarity : 0.004 0.039 4224 Dihedral : 14.127 161.363 3692 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.77 % Allowed : 16.82 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.15), residues: 2956 helix: 1.92 (0.11), residues: 2120 sheet: None (None), residues: 0 loop : -1.17 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 380 TYR 0.023 0.001 TYR C 150 PHE 0.012 0.001 PHE B 588 TRP 0.008 0.001 TRP D 334 HIS 0.004 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00327 (25084) covalent geometry : angle 0.53015 (33856) hydrogen bonds : bond 0.06620 ( 1516) hydrogen bonds : angle 3.75331 ( 4476) Misc. bond : bond 0.00031 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 275 time to evaluate : 0.827 Fit side-chains REVERT: A 48 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: A 57 LYS cc_start: 0.7966 (tttt) cc_final: 0.7519 (ttmt) REVERT: A 60 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6374 (mp0) REVERT: A 91 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: A 150 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8421 (p90) REVERT: A 191 ASP cc_start: 0.5971 (p0) cc_final: 0.5585 (m-30) REVERT: A 200 MET cc_start: 0.6994 (mtp) cc_final: 0.6398 (mmm) REVERT: A 380 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.5823 (mpp80) REVERT: A 409 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7403 (mm-30) REVERT: A 578 PHE cc_start: 0.7705 (t80) cc_final: 0.6953 (m-10) REVERT: A 579 LYS cc_start: 0.7768 (ttmm) cc_final: 0.7399 (ttmp) REVERT: A 805 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7577 (tttm) REVERT: B 48 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: B 57 LYS cc_start: 0.7972 (tttt) cc_final: 0.7525 (ttmt) REVERT: B 60 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6335 (mp0) REVERT: B 191 ASP cc_start: 0.5875 (p0) cc_final: 0.5458 (m-30) REVERT: B 200 MET cc_start: 0.7006 (mtp) cc_final: 0.6411 (mmm) REVERT: B 409 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7396 (mm-30) REVERT: B 576 ASP cc_start: 0.6409 (m-30) cc_final: 0.6060 (t0) REVERT: B 578 PHE cc_start: 0.7696 (t80) cc_final: 0.6957 (m-10) REVERT: B 579 LYS cc_start: 0.7778 (ttmm) cc_final: 0.7415 (ttmp) REVERT: B 805 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7589 (tttm) REVERT: C 48 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: C 57 LYS cc_start: 0.7966 (tttt) cc_final: 0.7521 (ttmt) REVERT: C 60 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: C 191 ASP cc_start: 0.5874 (p0) cc_final: 0.5465 (m-30) REVERT: C 200 MET cc_start: 0.7003 (mtp) cc_final: 0.6375 (mmm) REVERT: C 380 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.5805 (mpp80) REVERT: C 409 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7375 (mm-30) REVERT: C 576 ASP cc_start: 0.6402 (m-30) cc_final: 0.6053 (t0) REVERT: C 578 PHE cc_start: 0.7707 (t80) cc_final: 0.6962 (m-10) REVERT: C 579 LYS cc_start: 0.7769 (ttmm) cc_final: 0.7405 (ttmp) REVERT: D 48 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: D 57 LYS cc_start: 0.7961 (tttt) cc_final: 0.7513 (ttmt) REVERT: D 60 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6361 (mp0) REVERT: D 191 ASP cc_start: 0.6065 (p0) cc_final: 0.5650 (m-30) REVERT: D 200 MET cc_start: 0.7002 (mtp) cc_final: 0.6370 (mmm) REVERT: D 380 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.5700 (mpp80) REVERT: D 409 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7393 (mm-30) REVERT: D 439 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6679 (mpp) REVERT: D 576 ASP cc_start: 0.6424 (m-30) cc_final: 0.6116 (t0) REVERT: D 578 PHE cc_start: 0.7712 (t80) cc_final: 0.6959 (m-10) REVERT: D 579 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7375 (ttmp) REVERT: D 805 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7627 (tttt) outliers start: 99 outliers final: 47 residues processed: 346 average time/residue: 0.6781 time to fit residues: 268.7835 Evaluate side-chains 330 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 266 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 150 TYR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 805 LYS Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 805 LYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 380 ARG Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 572 ARG Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 799 VAL Chi-restraints excluded: chain D residue 805 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 200 optimal weight: 4.9990 chunk 223 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 271 optimal weight: 4.9990 chunk 275 optimal weight: 6.9990 chunk 290 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 214 optimal weight: 0.0980 chunk 111 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN C 809 GLN D 498 GLN ** D 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.222154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.175395 restraints weight = 25561.582| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.65 r_work: 0.3691 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 25088 Z= 0.164 Angle : 0.559 7.682 33856 Z= 0.288 Chirality : 0.040 0.119 3768 Planarity : 0.004 0.039 4224 Dihedral : 13.950 162.916 3692 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.61 % Allowed : 17.50 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.15), residues: 2956 helix: 1.77 (0.11), residues: 2148 sheet: None (None), residues: 0 loop : -1.16 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 785 TYR 0.023 0.001 TYR B 150 PHE 0.010 0.001 PHE A 611 TRP 0.008 0.001 TRP B 334 HIS 0.005 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00373 (25084) covalent geometry : angle 0.55878 (33856) hydrogen bonds : bond 0.06899 ( 1516) hydrogen bonds : angle 3.76507 ( 4476) Misc. bond : bond 0.00022 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 262 time to evaluate : 0.899 Fit side-chains REVERT: A 48 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: A 57 LYS cc_start: 0.7855 (tttt) cc_final: 0.7493 (ttmt) REVERT: A 60 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6453 (mp0) REVERT: A 91 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: A 191 ASP cc_start: 0.5905 (p0) cc_final: 0.5555 (m-30) REVERT: A 200 MET cc_start: 0.7047 (mtp) cc_final: 0.6471 (mmm) REVERT: A 380 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.5627 (mpp80) REVERT: A 409 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7340 (mm-30) REVERT: A 518 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6054 (mp0) REVERT: A 578 PHE cc_start: 0.7593 (t80) cc_final: 0.6923 (m-10) REVERT: A 579 LYS cc_start: 0.7797 (ttmm) cc_final: 0.7423 (ttmp) REVERT: A 805 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7565 (tttm) REVERT: B 48 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: B 57 LYS cc_start: 0.7861 (tttt) cc_final: 0.7497 (ttmt) REVERT: B 60 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: B 150 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8405 (p90) REVERT: B 191 ASP cc_start: 0.5914 (p0) cc_final: 0.5562 (m-30) REVERT: B 200 MET cc_start: 0.7043 (mtp) cc_final: 0.6468 (mmm) REVERT: B 380 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.5513 (mpp80) REVERT: B 409 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7330 (mm-30) REVERT: B 576 ASP cc_start: 0.6405 (m-30) cc_final: 0.6079 (t0) REVERT: B 578 PHE cc_start: 0.7600 (t80) cc_final: 0.6936 (m-10) REVERT: B 579 LYS cc_start: 0.7717 (ttmm) cc_final: 0.7334 (ttmp) REVERT: B 694 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8260 (mp) REVERT: B 805 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7576 (tttm) REVERT: C 48 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: C 57 LYS cc_start: 0.7868 (tttt) cc_final: 0.7504 (ttmt) REVERT: C 60 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6317 (mp0) REVERT: C 150 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8415 (p90) REVERT: C 191 ASP cc_start: 0.5920 (p0) cc_final: 0.5563 (m-30) REVERT: C 200 MET cc_start: 0.7063 (mtp) cc_final: 0.6473 (mmm) REVERT: C 380 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.5644 (mpp80) REVERT: C 409 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7343 (mm-30) REVERT: C 576 ASP cc_start: 0.6340 (m-30) cc_final: 0.6013 (t0) REVERT: C 578 PHE cc_start: 0.7601 (t80) cc_final: 0.6940 (m-10) REVERT: C 579 LYS cc_start: 0.7812 (ttmm) cc_final: 0.7419 (ttmp) REVERT: C 694 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8268 (mp) REVERT: D 48 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: D 57 LYS cc_start: 0.7864 (tttt) cc_final: 0.7509 (ttmt) REVERT: D 60 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6460 (mp0) REVERT: D 191 ASP cc_start: 0.5877 (p0) cc_final: 0.5563 (m-30) REVERT: D 200 MET cc_start: 0.7042 (mtp) cc_final: 0.6453 (mmm) REVERT: D 380 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.5691 (mpp80) REVERT: D 409 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7353 (mm-30) REVERT: D 576 ASP cc_start: 0.6427 (m-30) cc_final: 0.6124 (t0) REVERT: D 578 PHE cc_start: 0.7567 (t80) cc_final: 0.6919 (m-10) REVERT: D 579 LYS cc_start: 0.7792 (ttmm) cc_final: 0.7399 (ttmp) REVERT: D 694 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8250 (mp) REVERT: D 805 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7538 (tttt) outliers start: 95 outliers final: 53 residues processed: 328 average time/residue: 0.6601 time to fit residues: 247.9898 Evaluate side-chains 332 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 258 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 805 LYS Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 805 LYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 380 ARG Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 572 ARG Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 799 VAL Chi-restraints excluded: chain D residue 805 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 293 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 87 optimal weight: 0.0040 chunk 258 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 ASN C 776 GLN ** D 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.223329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.176651 restraints weight = 25765.073| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.67 r_work: 0.3708 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 25088 Z= 0.143 Angle : 0.528 8.785 33856 Z= 0.272 Chirality : 0.039 0.118 3768 Planarity : 0.004 0.040 4224 Dihedral : 13.623 161.286 3692 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.35 % Allowed : 18.34 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.15), residues: 2956 helix: 1.90 (0.11), residues: 2148 sheet: None (None), residues: 0 loop : -1.10 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 815 TYR 0.022 0.001 TYR A 150 PHE 0.011 0.001 PHE B 588 TRP 0.008 0.001 TRP C 334 HIS 0.004 0.001 HIS D 169 Details of bonding type rmsd covalent geometry : bond 0.00314 (25084) covalent geometry : angle 0.52803 (33856) hydrogen bonds : bond 0.06311 ( 1516) hydrogen bonds : angle 3.68111 ( 4476) Misc. bond : bond 0.00008 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 266 time to evaluate : 0.921 Fit side-chains REVERT: A 48 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: A 57 LYS cc_start: 0.7925 (tttt) cc_final: 0.7448 (ttmt) REVERT: A 60 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6247 (mp0) REVERT: A 91 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: A 191 ASP cc_start: 0.5916 (p0) cc_final: 0.5586 (m-30) REVERT: A 200 MET cc_start: 0.7042 (mtp) cc_final: 0.6481 (mmm) REVERT: A 380 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.5653 (mpp80) REVERT: A 409 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7356 (mm-30) REVERT: A 518 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6033 (mp0) REVERT: A 576 ASP cc_start: 0.6528 (m-30) cc_final: 0.6183 (OUTLIER) REVERT: A 578 PHE cc_start: 0.7477 (t80) cc_final: 0.6881 (m-10) REVERT: A 579 LYS cc_start: 0.7699 (ttmm) cc_final: 0.7290 (ttmp) REVERT: A 805 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7372 (tttm) REVERT: B 48 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: B 57 LYS cc_start: 0.7930 (tttt) cc_final: 0.7460 (ttmt) REVERT: B 60 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: B 191 ASP cc_start: 0.5918 (p0) cc_final: 0.5591 (m-30) REVERT: B 200 MET cc_start: 0.7051 (mtp) cc_final: 0.6493 (mmm) REVERT: B 380 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.5514 (mpp80) REVERT: B 576 ASP cc_start: 0.6370 (m-30) cc_final: 0.6069 (t0) REVERT: B 578 PHE cc_start: 0.7487 (t80) cc_final: 0.6893 (m-10) REVERT: B 579 LYS cc_start: 0.7741 (ttmm) cc_final: 0.7329 (ttmp) REVERT: B 684 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6790 (tp30) REVERT: B 805 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7366 (tttm) REVERT: C 48 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: C 57 LYS cc_start: 0.7935 (tttt) cc_final: 0.7464 (ttmt) REVERT: C 60 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6234 (mp0) REVERT: C 191 ASP cc_start: 0.5925 (p0) cc_final: 0.5594 (m-30) REVERT: C 200 MET cc_start: 0.7065 (mtp) cc_final: 0.6497 (mmm) REVERT: C 380 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.5638 (mpp80) REVERT: C 409 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7345 (mm-30) REVERT: C 576 ASP cc_start: 0.6309 (m-30) cc_final: 0.6009 (t0) REVERT: C 578 PHE cc_start: 0.7492 (t80) cc_final: 0.6898 (m-10) REVERT: C 579 LYS cc_start: 0.7720 (ttmm) cc_final: 0.7320 (ttmp) REVERT: C 684 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6788 (tp30) REVERT: D 48 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: D 57 LYS cc_start: 0.7925 (tttt) cc_final: 0.7452 (ttmt) REVERT: D 60 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6238 (mp0) REVERT: D 191 ASP cc_start: 0.5905 (p0) cc_final: 0.5577 (m-30) REVERT: D 200 MET cc_start: 0.7044 (mtp) cc_final: 0.6475 (mmm) REVERT: D 380 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.5650 (mpp80) REVERT: D 409 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7358 (mm-30) REVERT: D 576 ASP cc_start: 0.6425 (m-30) cc_final: 0.6137 (t0) REVERT: D 578 PHE cc_start: 0.7486 (t80) cc_final: 0.6887 (m-10) REVERT: D 579 LYS cc_start: 0.7702 (ttmm) cc_final: 0.7310 (ttmp) outliers start: 88 outliers final: 49 residues processed: 323 average time/residue: 0.6842 time to fit residues: 251.6551 Evaluate side-chains 324 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 261 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 805 LYS Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 805 LYS Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 380 ARG Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 572 ARG Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 670 ILE Chi-restraints excluded: chain D residue 799 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 272 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 288 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.220980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.174619 restraints weight = 25820.638| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.83 r_work: 0.3659 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25088 Z= 0.185 Angle : 0.590 8.820 33856 Z= 0.303 Chirality : 0.040 0.116 3768 Planarity : 0.004 0.039 4224 Dihedral : 13.643 162.765 3692 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.35 % Allowed : 18.65 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.15), residues: 2956 helix: 1.84 (0.11), residues: 2116 sheet: None (None), residues: 0 loop : -1.02 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 428 TYR 0.024 0.002 TYR B 150 PHE 0.012 0.002 PHE D 588 TRP 0.010 0.002 TRP D 334 HIS 0.005 0.001 HIS D 169 Details of bonding type rmsd covalent geometry : bond 0.00433 (25084) covalent geometry : angle 0.58975 (33856) hydrogen bonds : bond 0.07281 ( 1516) hydrogen bonds : angle 3.79198 ( 4476) Misc. bond : bond 0.00033 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 266 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: A 57 LYS cc_start: 0.7872 (tttt) cc_final: 0.7481 (ttmt) REVERT: A 60 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: A 191 ASP cc_start: 0.5875 (p0) cc_final: 0.5521 (m-30) REVERT: A 200 MET cc_start: 0.7016 (mtp) cc_final: 0.6492 (mmm) REVERT: A 409 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7345 (mm-30) REVERT: A 578 PHE cc_start: 0.7521 (t80) cc_final: 0.6931 (m-10) REVERT: A 579 LYS cc_start: 0.7734 (ttmm) cc_final: 0.7330 (ttmp) REVERT: B 48 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: B 57 LYS cc_start: 0.7863 (tttt) cc_final: 0.7477 (ttmt) REVERT: B 60 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: B 191 ASP cc_start: 0.5877 (p0) cc_final: 0.5520 (m-30) REVERT: B 200 MET cc_start: 0.7012 (mtp) cc_final: 0.6487 (mmm) REVERT: B 380 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.5504 (mpp80) REVERT: B 576 ASP cc_start: 0.6341 (m-30) cc_final: 0.6018 (t0) REVERT: B 578 PHE cc_start: 0.7524 (t80) cc_final: 0.6936 (m-10) REVERT: B 579 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7325 (ttmp) REVERT: B 684 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6776 (tp30) REVERT: C 48 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: C 57 LYS cc_start: 0.7875 (tttt) cc_final: 0.7487 (ttmt) REVERT: C 60 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: C 191 ASP cc_start: 0.5883 (p0) cc_final: 0.5528 (m-30) REVERT: C 200 MET cc_start: 0.7040 (mtp) cc_final: 0.6505 (mmm) REVERT: C 409 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7333 (mm-30) REVERT: C 576 ASP cc_start: 0.6362 (m-30) cc_final: 0.6052 (OUTLIER) REVERT: C 578 PHE cc_start: 0.7513 (t80) cc_final: 0.6938 (m-10) REVERT: C 579 LYS cc_start: 0.7740 (ttmm) cc_final: 0.7479 (ttmp) REVERT: C 684 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6772 (tp30) REVERT: D 48 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: D 57 LYS cc_start: 0.7869 (tttt) cc_final: 0.7480 (ttmt) REVERT: D 60 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6530 (mp0) REVERT: D 191 ASP cc_start: 0.5933 (p0) cc_final: 0.5567 (m-30) REVERT: D 200 MET cc_start: 0.7005 (mtp) cc_final: 0.6472 (mmm) REVERT: D 380 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.5648 (mpp80) REVERT: D 409 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7343 (mm-30) REVERT: D 576 ASP cc_start: 0.6566 (m-30) cc_final: 0.6297 (t0) REVERT: D 578 PHE cc_start: 0.7502 (t80) cc_final: 0.6932 (m-10) REVERT: D 579 LYS cc_start: 0.7697 (ttmm) cc_final: 0.7275 (ttmp) outliers start: 88 outliers final: 54 residues processed: 327 average time/residue: 0.6990 time to fit residues: 260.9628 Evaluate side-chains 327 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 264 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 799 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 228 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 260 optimal weight: 0.3980 chunk 97 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 ASN ** B 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN D 389 HIS D 403 ASN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.222889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.174759 restraints weight = 25582.451| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.40 r_work: 0.3720 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25088 Z= 0.149 Angle : 0.542 9.173 33856 Z= 0.279 Chirality : 0.039 0.117 3768 Planarity : 0.004 0.039 4224 Dihedral : 13.459 161.751 3692 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.47 % Allowed : 19.56 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.16), residues: 2956 helix: 1.89 (0.11), residues: 2144 sheet: None (None), residues: 0 loop : -0.99 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 815 TYR 0.020 0.001 TYR B 150 PHE 0.011 0.001 PHE B 588 TRP 0.008 0.001 TRP C 334 HIS 0.005 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00330 (25084) covalent geometry : angle 0.54187 (33856) hydrogen bonds : bond 0.06462 ( 1516) hydrogen bonds : angle 3.70391 ( 4476) Misc. bond : bond 0.00006 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 260 time to evaluate : 0.883 Fit side-chains REVERT: A 48 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: A 57 LYS cc_start: 0.7946 (tttt) cc_final: 0.7510 (ttmt) REVERT: A 60 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: A 91 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: A 191 ASP cc_start: 0.5941 (p0) cc_final: 0.5636 (m-30) REVERT: A 200 MET cc_start: 0.7121 (mtp) cc_final: 0.6616 (mmm) REVERT: A 578 PHE cc_start: 0.7535 (t80) cc_final: 0.6993 (m-10) REVERT: A 579 LYS cc_start: 0.7788 (ttmm) cc_final: 0.7368 (ttmp) REVERT: B 48 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: B 57 LYS cc_start: 0.7950 (tttt) cc_final: 0.7530 (ttmt) REVERT: B 60 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6427 (mp0) REVERT: B 191 ASP cc_start: 0.5938 (p0) cc_final: 0.5636 (m-30) REVERT: B 200 MET cc_start: 0.7118 (mtp) cc_final: 0.6611 (mmm) REVERT: B 380 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.5531 (mpp80) REVERT: B 576 ASP cc_start: 0.6379 (m-30) cc_final: 0.6076 (t0) REVERT: B 578 PHE cc_start: 0.7538 (t80) cc_final: 0.6993 (m-10) REVERT: B 579 LYS cc_start: 0.7800 (ttmm) cc_final: 0.7376 (ttmp) REVERT: C 48 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: C 57 LYS cc_start: 0.7952 (tttt) cc_final: 0.7528 (ttmt) REVERT: C 60 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: C 191 ASP cc_start: 0.5948 (p0) cc_final: 0.5648 (m-30) REVERT: C 200 MET cc_start: 0.7142 (mtp) cc_final: 0.6631 (mmm) REVERT: C 380 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.5660 (mpp80) REVERT: C 576 ASP cc_start: 0.6395 (m-30) cc_final: 0.6103 (OUTLIER) REVERT: C 578 PHE cc_start: 0.7538 (t80) cc_final: 0.6993 (m-10) REVERT: C 579 LYS cc_start: 0.7807 (ttmm) cc_final: 0.7394 (ttmp) REVERT: C 684 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6759 (tp30) REVERT: D 48 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: D 57 LYS cc_start: 0.7936 (tttt) cc_final: 0.7514 (ttmt) REVERT: D 60 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: D 191 ASP cc_start: 0.5943 (p0) cc_final: 0.5643 (m-30) REVERT: D 200 MET cc_start: 0.7114 (mtp) cc_final: 0.6602 (mmm) REVERT: D 380 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.5713 (mpp80) REVERT: D 576 ASP cc_start: 0.6596 (m-30) cc_final: 0.6351 (t0) REVERT: D 578 PHE cc_start: 0.7507 (t80) cc_final: 0.6986 (m-10) REVERT: D 579 LYS cc_start: 0.7773 (ttmm) cc_final: 0.7371 (ttmp) outliers start: 65 outliers final: 49 residues processed: 306 average time/residue: 0.7075 time to fit residues: 246.9297 Evaluate side-chains 315 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 380 ARG Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 150 TYR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 380 ARG Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 799 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 255 optimal weight: 0.0870 chunk 18 optimal weight: 0.3980 chunk 187 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 44 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 52 optimal weight: 0.0980 chunk 139 optimal weight: 0.9980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 809 GLN C 800 ASN D 389 HIS ** D 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.229353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.172364 restraints weight = 25639.976| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.19 r_work: 0.3826 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25088 Z= 0.105 Angle : 0.484 9.135 33856 Z= 0.247 Chirality : 0.037 0.117 3768 Planarity : 0.003 0.041 4224 Dihedral : 12.864 160.699 3692 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.05 % Allowed : 20.05 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.16), residues: 2956 helix: 2.27 (0.11), residues: 2152 sheet: None (None), residues: 0 loop : -0.83 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 815 TYR 0.008 0.001 TYR C 192 PHE 0.010 0.001 PHE B 588 TRP 0.012 0.001 TRP B 693 HIS 0.001 0.000 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00201 (25084) covalent geometry : angle 0.48412 (33856) hydrogen bonds : bond 0.04595 ( 1516) hydrogen bonds : angle 3.51309 ( 4476) Misc. bond : bond 0.00020 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9390.59 seconds wall clock time: 160 minutes 33.04 seconds (9633.04 seconds total)