Starting phenix.real_space_refine on Fri Jun 27 05:56:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rsc_19476/06_2025/8rsc_19476.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rsc_19476/06_2025/8rsc_19476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rsc_19476/06_2025/8rsc_19476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rsc_19476/06_2025/8rsc_19476.map" model { file = "/net/cci-nas-00/data/ceres_data/8rsc_19476/06_2025/8rsc_19476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rsc_19476/06_2025/8rsc_19476.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 20 5.49 5 S 138 5.16 5 C 19758 2.51 5 N 5773 2.21 5 O 6185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31874 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5285 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 704} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 316 Chain: "B" Number of atoms: 5262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5262 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 701} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 583 Unresolved non-hydrogen angles: 741 Unresolved non-hydrogen dihedrals: 465 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 315 Chain: "C" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5267 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 700} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 569 Unresolved non-hydrogen angles: 723 Unresolved non-hydrogen dihedrals: 455 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 303 Chain: "D" Number of atoms: 5263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5263 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 700} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 573 Unresolved non-hydrogen angles: 728 Unresolved non-hydrogen dihedrals: 458 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 307 Chain: "E" Number of atoms: 5260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5260 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 700} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 732 Unresolved non-hydrogen dihedrals: 460 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 310 Chain: "F" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5267 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 700} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 569 Unresolved non-hydrogen angles: 723 Unresolved non-hydrogen dihedrals: 455 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 303 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.26, per 1000 atoms: 0.60 Number of scatterers: 31874 At special positions: 0 Unit cell: (169.42, 174.58, 118.68, 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 138 16.00 P 20 15.00 O 6185 8.00 N 5773 7.00 C 19758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.71 Conformation dependent library (CDL) restraints added in 4.2 seconds 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8338 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 34 sheets defined 50.2% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.668A pdb=" N GLU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.129A pdb=" N ASN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.698A pdb=" N PHE A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 202 Processing helix chain 'A' and resid 203 through 206 removed outlier: 4.064A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 206' Processing helix chain 'A' and resid 209 through 226 removed outlier: 3.556A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.938A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 278 through 295 removed outlier: 3.727A pdb=" N LEU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 319 through 333 removed outlier: 4.082A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.643A pdb=" N SER A 352 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 353' Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.744A pdb=" N ALA A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 427 removed outlier: 3.695A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.930A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.731A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.094A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.623A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 removed outlier: 4.055A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 554 removed outlier: 3.632A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 4.267A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 600 through 610 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.835A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.595A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 688 Processing helix chain 'A' and resid 689 through 716 removed outlier: 3.902A pdb=" N ARG A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.591A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 762 removed outlier: 3.658A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.689A pdb=" N ASP B 205 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 3.910A pdb=" N LEU B 213 " --> pdb=" O CYS B 209 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.841A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 278 through 295 removed outlier: 4.091A pdb=" N GLU B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 319 through 334 removed outlier: 3.566A pdb=" N ILE B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.551A pdb=" N SER B 352 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 353' Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 396 through 402 removed outlier: 3.648A pdb=" N ALA B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.521A pdb=" N ALA B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 4.802A pdb=" N GLU B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP B 434 " --> pdb=" O ILE B 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 434' Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.951A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.737A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 3.659A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.612A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 536 removed outlier: 4.077A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS B 529 " --> pdb=" O THR B 525 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 554 removed outlier: 3.682A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 4.297A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 600 through 610 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.536A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.552A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 716 removed outlier: 4.380A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.644A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 762 removed outlier: 3.537A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 47 removed outlier: 3.756A pdb=" N MET C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP C 47 " --> pdb=" O PRO C 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 43 through 47' Processing helix chain 'C' and resid 85 through 93 removed outlier: 4.117A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 removed outlier: 3.838A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.632A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 278 through 296 removed outlier: 4.074A pdb=" N ARG C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 318 through 336 removed outlier: 3.594A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS C 336 " --> pdb=" O MET C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.877A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.680A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 432 removed outlier: 3.760A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 removed outlier: 3.980A pdb=" N LEU C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.037A pdb=" N LEU C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 506 removed outlier: 4.200A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 removed outlier: 3.691A pdb=" N LEU C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS C 529 " --> pdb=" O THR C 525 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 554 removed outlier: 3.530A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 4.340A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.885A pdb=" N ASN C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 615 removed outlier: 3.586A pdb=" N LYS C 615 " --> pdb=" O SER C 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 612 through 615' Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.679A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 removed outlier: 3.693A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 716 removed outlier: 3.604A pdb=" N LEU C 687 " --> pdb=" O SER C 683 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 713 " --> pdb=" O ARG C 709 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR C 715 " --> pdb=" O ARG C 711 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN C 716 " --> pdb=" O GLU C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.677A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 762 removed outlier: 3.762A pdb=" N LEU C 762 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 removed outlier: 3.856A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 136 removed outlier: 4.181A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 226 removed outlier: 5.165A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 232 removed outlier: 3.989A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 278 through 296 Processing helix chain 'D' and resid 305 through 309 Processing helix chain 'D' and resid 318 through 338 removed outlier: 3.523A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 329 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS D 336 " --> pdb=" O MET D 332 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN D 337 " --> pdb=" O ASP D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.888A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 removed outlier: 4.003A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 432 removed outlier: 4.496A pdb=" N LYS D 425 " --> pdb=" O GLN D 421 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 removed outlier: 3.960A pdb=" N LEU D 445 " --> pdb=" O VAL D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 482 through 499 removed outlier: 3.952A pdb=" N LEU D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 506 removed outlier: 4.146A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 removed outlier: 3.523A pdb=" N LEU D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS D 529 " --> pdb=" O THR D 525 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 554 removed outlier: 3.582A pdb=" N LEU D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 4.368A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 removed outlier: 3.758A pdb=" N ASN D 602 " --> pdb=" O ASP D 598 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 615 removed outlier: 3.649A pdb=" N LYS D 615 " --> pdb=" O SER D 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 612 through 615' Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.543A pdb=" N ILE D 628 " --> pdb=" O ARG D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.614A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 removed outlier: 3.525A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 716 removed outlier: 3.662A pdb=" N LEU D 687 " --> pdb=" O SER D 683 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 713 " --> pdb=" O ARG D 709 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR D 715 " --> pdb=" O ARG D 711 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN D 716 " --> pdb=" O GLU D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 3.769A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 762 removed outlier: 3.864A pdb=" N LEU D 762 " --> pdb=" O PHE D 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 91 Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.619A pdb=" N VAL E 123 " --> pdb=" O ASP E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 140 removed outlier: 3.765A pdb=" N VAL E 133 " --> pdb=" O ASN E 129 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.516A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 221 Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 226 through 233 Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 278 through 296 removed outlier: 4.007A pdb=" N ARG E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.717A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 318 through 336 removed outlier: 3.643A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.814A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 402 removed outlier: 4.072A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 400 " --> pdb=" O LEU E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 435 removed outlier: 5.725A pdb=" N LYS E 425 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU E 433 " --> pdb=" O LEU E 429 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP E 434 " --> pdb=" O ILE E 430 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 removed outlier: 3.955A pdb=" N LEU E 445 " --> pdb=" O VAL E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 482 through 499 removed outlier: 3.913A pdb=" N LEU E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 4.293A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU E 504 " --> pdb=" O PRO E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 removed outlier: 4.025A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS E 529 " --> pdb=" O THR E 525 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 554 removed outlier: 3.530A pdb=" N LEU E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 569 removed outlier: 3.849A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 removed outlier: 3.756A pdb=" N ASN E 602 " --> pdb=" O ASP E 598 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 615 removed outlier: 3.776A pdb=" N LYS E 615 " --> pdb=" O SER E 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 612 through 615' Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.940A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 662 removed outlier: 3.627A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 716 removed outlier: 3.637A pdb=" N LEU E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG E 713 " --> pdb=" O ARG E 709 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN E 714 " --> pdb=" O GLU E 710 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR E 715 " --> pdb=" O ARG E 711 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN E 716 " --> pdb=" O GLU E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 743 removed outlier: 3.754A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 762 removed outlier: 3.866A pdb=" N LEU E 762 " --> pdb=" O PHE E 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 129 through 140 removed outlier: 4.330A pdb=" N VAL F 133 " --> pdb=" O ASN F 129 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 221 Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 278 through 296 removed outlier: 4.123A pdb=" N ARG F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.710A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 318 through 336 removed outlier: 3.513A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER F 326 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU F 328 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS F 336 " --> pdb=" O MET F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.795A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.820A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 430 removed outlier: 3.656A pdb=" N ALA F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 435 removed outlier: 4.241A pdb=" N ASP F 434 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 430 through 435' Processing helix chain 'F' and resid 438 through 445 removed outlier: 3.819A pdb=" N LEU F 445 " --> pdb=" O VAL F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.530A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 3.505A pdb=" N LYS F 486 " --> pdb=" O LEU F 482 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 4.030A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 removed outlier: 3.939A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS F 529 " --> pdb=" O THR F 525 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 554 removed outlier: 3.515A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 569 removed outlier: 4.409A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 removed outlier: 4.081A pdb=" N ASN F 602 " --> pdb=" O ASP F 598 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 615 removed outlier: 3.640A pdb=" N LYS F 615 " --> pdb=" O SER F 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 612 through 615' Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.618A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 removed outlier: 3.615A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 716 removed outlier: 3.661A pdb=" N LEU F 687 " --> pdb=" O SER F 683 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG F 713 " --> pdb=" O ARG F 709 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN F 714 " --> pdb=" O GLU F 710 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR F 715 " --> pdb=" O ARG F 711 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN F 716 " --> pdb=" O GLU F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.725A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 762 removed outlier: 3.747A pdb=" N LEU F 762 " --> pdb=" O PHE F 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.628A pdb=" N LEU A 26 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 270 removed outlier: 3.665A pdb=" N ILE A 342 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N THR A 347 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 243 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 542 Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 60 Processing sheet with id=AA6, first strand: chain 'B' and resid 117 through 118 removed outlier: 4.342A pdb=" N LEU B 117 " --> pdb=" O LYS B 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.504A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 342 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 241 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N THR B 347 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 243 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.731A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AB1, first strand: chain 'C' and resid 65 through 69 Processing sheet with id=AB2, first strand: chain 'C' and resid 116 through 118 Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.442A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE C 241 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR C 347 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU C 243 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.788A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 26 through 27 Processing sheet with id=AB7, first strand: chain 'D' and resid 65 through 70 Processing sheet with id=AB8, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AB9, first strand: chain 'D' and resid 153 through 156 Processing sheet with id=AC1, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.450A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE D 241 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR D 347 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU D 243 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.767A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 26 through 27 Processing sheet with id=AC4, first strand: chain 'E' and resid 65 through 70 Processing sheet with id=AC5, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AC6, first strand: chain 'E' and resid 116 through 118 Processing sheet with id=AC7, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.518A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE E 241 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR E 347 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU E 243 " --> pdb=" O THR E 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.816A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 26 through 27 Processing sheet with id=AD1, first strand: chain 'F' and resid 41 through 42 removed outlier: 5.381A pdb=" N LEU F 41 " --> pdb=" O ASP F 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 65 through 69 Processing sheet with id=AD3, first strand: chain 'F' and resid 110 through 111 Processing sheet with id=AD4, first strand: chain 'F' and resid 116 through 117 Processing sheet with id=AD5, first strand: chain 'F' and resid 153 through 156 Processing sheet with id=AD6, first strand: chain 'F' and resid 265 through 270 removed outlier: 3.737A pdb=" N ASP F 304 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE F 241 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR F 347 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU F 243 " --> pdb=" O THR F 347 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.809A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) 1376 hydrogen bonds defined for protein. 3867 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: 12.06 Time building geometry restraints manager: 9.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6184 1.32 - 1.45: 6967 1.45 - 1.57: 18904 1.57 - 1.69: 31 1.69 - 1.81: 234 Bond restraints: 32320 Sorted by residual: bond pdb=" CA ARG A 191 " pdb=" C ARG A 191 " ideal model delta sigma weight residual 1.531 1.488 0.043 1.12e-02 7.97e+03 1.49e+01 bond pdb=" CA GLU B 200 " pdb=" C GLU B 200 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.10e-02 8.26e+03 1.11e+01 bond pdb=" CG GLU A 402 " pdb=" CD GLU A 402 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.00e+01 bond pdb=" N ARG A 191 " pdb=" CA ARG A 191 " ideal model delta sigma weight residual 1.462 1.433 0.029 1.23e-02 6.61e+03 5.51e+00 bond pdb=" N VAL B 201 " pdb=" CA VAL B 201 " ideal model delta sigma weight residual 1.461 1.434 0.027 1.17e-02 7.31e+03 5.48e+00 ... (remaining 32315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 43452 2.61 - 5.22: 413 5.22 - 7.83: 53 7.83 - 10.44: 4 10.44 - 13.05: 3 Bond angle restraints: 43925 Sorted by residual: angle pdb=" C ALA D 339 " pdb=" N HIS D 340 " pdb=" CA HIS D 340 " ideal model delta sigma weight residual 122.34 135.39 -13.05 1.39e+00 5.18e-01 8.81e+01 angle pdb=" C PRO B 223 " pdb=" N LEU B 224 " pdb=" CA LEU B 224 " ideal model delta sigma weight residual 120.44 132.16 -11.72 1.36e+00 5.41e-01 7.42e+01 angle pdb=" N GLU A 192 " pdb=" CA GLU A 192 " pdb=" C GLU A 192 " ideal model delta sigma weight residual 111.28 102.51 8.77 1.09e+00 8.42e-01 6.48e+01 angle pdb=" C ARG E 638 " pdb=" N LEU E 639 " pdb=" CA LEU E 639 " ideal model delta sigma weight residual 122.16 134.12 -11.96 1.50e+00 4.44e-01 6.35e+01 angle pdb=" N VAL B 201 " pdb=" CA VAL B 201 " pdb=" C VAL B 201 " ideal model delta sigma weight residual 110.42 116.56 -6.14 9.60e-01 1.09e+00 4.09e+01 ... (remaining 43920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.01: 18223 22.01 - 44.02: 1367 44.02 - 66.02: 185 66.02 - 88.03: 48 88.03 - 110.04: 8 Dihedral angle restraints: 19831 sinusoidal: 7006 harmonic: 12825 Sorted by residual: dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual -60.00 -170.04 110.04 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" CA ARG A 144 " pdb=" C ARG A 144 " pdb=" N PRO A 145 " pdb=" CA PRO A 145 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ILE E 423 " pdb=" C ILE E 423 " pdb=" N ARG E 424 " pdb=" CA ARG E 424 " ideal model delta harmonic sigma weight residual -180.00 -152.84 -27.16 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 19828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4284 0.055 - 0.111: 686 0.111 - 0.166: 130 0.166 - 0.221: 4 0.221 - 0.277: 3 Chirality restraints: 5107 Sorted by residual: chirality pdb=" CA GLU A 194 " pdb=" N GLU A 194 " pdb=" C GLU A 194 " pdb=" CB GLU A 194 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA VAL F 201 " pdb=" N VAL F 201 " pdb=" C VAL F 201 " pdb=" CB VAL F 201 " both_signs ideal model delta sigma weight residual False 2.44 2.20 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE B 189 " pdb=" N ILE B 189 " pdb=" C ILE B 189 " pdb=" CB ILE B 189 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 5104 not shown) Planarity restraints: 5890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 222 " 0.048 5.00e-02 4.00e+02 7.39e-02 8.75e+00 pdb=" N PRO B 223 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 223 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 223 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 635 " 0.050 5.00e-02 4.00e+02 7.30e-02 8.52e+00 pdb=" N PRO E 636 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 636 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 636 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 398 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.50e+00 pdb=" C GLN A 398 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN A 398 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL A 399 " 0.017 2.00e-02 2.50e+03 ... (remaining 5887 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 308 2.58 - 3.16: 27662 3.16 - 3.74: 46395 3.74 - 4.32: 59953 4.32 - 4.90: 100966 Nonbonded interactions: 235284 Sorted by model distance: nonbonded pdb=" OH TYR D 244 " pdb=" OE1 GLN D 568 " model vdw 1.995 3.040 nonbonded pdb=" O GLU A 440 " pdb=" OG SER A 444 " model vdw 2.010 3.040 nonbonded pdb=" OG1 THR B 448 " pdb=" OD1 ASP B 450 " model vdw 2.089 3.040 nonbonded pdb=" O ALA C 455 " pdb=" OG SER C 459 " model vdw 2.099 3.040 nonbonded pdb=" NH1 ARG A 377 " pdb=" O THR A 403 " model vdw 2.118 3.120 ... (remaining 235279 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 21 through 204 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB )) or resid 206 through 759 or (resid 760 and (name N o \ r name CA or name C or name O or name CB )) or resid 761 through 762 or resid 90 \ 1)) selection = (chain 'B' and (resid 21 through 204 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB )) or resid 206 through 762 or resid 901)) selection = (chain 'C' and ((resid 21 through 201 and (name N or name CA or name C or name O \ or name CB )) or resid 202 through 204 or (resid 205 and (name N or name CA or \ name C or name O or name CB )) or resid 206 through 759 or (resid 760 and (name \ N or name CA or name C or name O or name CB )) or resid 761 through 762 or resid \ 902)) selection = (chain 'D' and ((resid 21 through 201 and (name N or name CA or name C or name O \ or name CB )) or resid 202 through 204 or (resid 205 and (name N or name CA or \ name C or name O or name CB )) or resid 206 through 759 or (resid 760 and (name \ N or name CA or name C or name O or name CB )) or resid 761 through 762 or resid \ 902)) selection = (chain 'E' and ((resid 21 through 201 and (name N or name CA or name C or name O \ or name CB )) or resid 202 through 759 or (resid 760 and (name N or name CA or \ name C or name O or name CB )) or resid 761 through 762 or resid 902)) selection = (chain 'F' and ((resid 21 through 201 and (name N or name CA or name C or name O \ or name CB )) or resid 202 through 204 or (resid 205 and (name N or name CA or \ name C or name O or name CB )) or resid 206 through 759 or (resid 760 and (name \ N or name CA or name C or name O or name CB )) or resid 761 through 762 or resid \ 902)) } 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 group one per residue 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: 2.090 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: 0.040 Extract box with map and model: 1.190 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 70.820 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 32320 Z= 0.162 Angle : 0.643 13.047 43925 Z= 0.360 Chirality : 0.042 0.277 5107 Planarity : 0.004 0.074 5890 Dihedral : 15.625 110.038 11493 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.04 % Favored : 92.94 % Rotamer: Outliers : 0.11 % Allowed : 15.96 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.13), residues: 4445 helix: 0.38 (0.13), residues: 1779 sheet: -0.57 (0.22), residues: 586 loop : -2.34 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 454 HIS 0.003 0.001 HIS A 499 PHE 0.010 0.001 PHE E 674 TYR 0.011 0.001 TYR B 244 ARG 0.003 0.000 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.18485 ( 1376) hydrogen bonds : angle 7.09493 ( 3867) covalent geometry : bond 0.00295 (32320) covalent geometry : angle 0.64285 (43925) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 354 time to evaluate : 3.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 734 ASP cc_start: 0.5873 (p0) cc_final: 0.4770 (t70) REVERT: C 403 THR cc_start: 0.8098 (m) cc_final: 0.7878 (m) REVERT: C 465 ARG cc_start: 0.6745 (mmp80) cc_final: 0.6527 (ptm-80) REVERT: D 465 ARG cc_start: 0.6452 (mmp80) cc_final: 0.6074 (ttm170) REVERT: D 745 ARG cc_start: 0.6101 (mtp-110) cc_final: 0.5712 (mtt180) outliers start: 3 outliers final: 3 residues processed: 357 average time/residue: 0.4561 time to fit residues: 257.6852 Evaluate side-chains 327 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 324 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain F residue 568 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 20.0000 chunk 336 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 227 optimal weight: 40.0000 chunk 179 optimal weight: 5.9990 chunk 348 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 211 optimal weight: 0.9990 chunk 259 optimal weight: 3.9990 chunk 403 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 406 HIS ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 382 GLN B 499 HIS C 317 HIS C 340 HIS C 714 GLN D 215 GLN D 382 GLN D 616 ASN D 714 GLN F 404 HIS F 558 ASN F 568 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.180600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150870 restraints weight = 43172.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149918 restraints weight = 78542.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.151310 restraints weight = 71718.893| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 32320 Z= 0.200 Angle : 0.702 10.797 43925 Z= 0.355 Chirality : 0.048 0.194 5107 Planarity : 0.005 0.067 5890 Dihedral : 6.309 94.443 4843 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.83 % Favored : 94.15 % Rotamer: Outliers : 2.68 % Allowed : 15.21 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 4445 helix: 0.39 (0.12), residues: 1836 sheet: -0.39 (0.22), residues: 589 loop : -1.99 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 476 HIS 0.007 0.002 HIS F 735 PHE 0.024 0.002 PHE C 575 TYR 0.030 0.002 TYR B 203 ARG 0.014 0.001 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.05442 ( 1376) hydrogen bonds : angle 5.15255 ( 3867) covalent geometry : bond 0.00473 (32320) covalent geometry : angle 0.70173 (43925) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 374 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8415 (mt) REVERT: B 273 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7422 (mt-10) REVERT: B 639 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8009 (mt) REVERT: C 465 ARG cc_start: 0.6869 (mmp80) cc_final: 0.6539 (ptm-80) REVERT: C 534 GLU cc_start: 0.6526 (tm-30) cc_final: 0.6081 (tm-30) REVERT: C 720 MET cc_start: 0.3195 (tpt) cc_final: 0.2752 (tpt) REVERT: D 389 LYS cc_start: 0.7377 (tptp) cc_final: 0.6749 (mtmt) REVERT: D 449 MET cc_start: 0.7118 (tpt) cc_final: 0.6751 (tpt) REVERT: D 465 ARG cc_start: 0.6424 (mmp80) cc_final: 0.5993 (ttm170) REVERT: D 508 MET cc_start: 0.3898 (tpt) cc_final: 0.3375 (tpt) REVERT: D 722 VAL cc_start: -0.2723 (OUTLIER) cc_final: -0.2941 (t) REVERT: F 542 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8284 (mp) REVERT: F 598 ASP cc_start: 0.7875 (p0) cc_final: 0.7656 (p0) REVERT: F 641 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7862 (mp10) outliers start: 75 outliers final: 41 residues processed: 424 average time/residue: 0.5066 time to fit residues: 345.8225 Evaluate side-chains 360 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 314 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 641 GLN Chi-restraints excluded: chain F residue 703 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 103 optimal weight: 10.0000 chunk 274 optimal weight: 0.8980 chunk 339 optimal weight: 10.0000 chunk 284 optimal weight: 3.9990 chunk 403 optimal weight: 10.0000 chunk 424 optimal weight: 5.9990 chunk 335 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 361 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS A 327 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN C 285 ASN C 340 HIS C 406 HIS C 490 GLN D 285 ASN D 382 GLN D 589 ASN D 616 ASN D 660 ASN D 692 GLN F 337 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.177634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143596 restraints weight = 43359.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142964 restraints weight = 69769.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144597 restraints weight = 60585.298| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32320 Z= 0.185 Angle : 0.662 6.844 43925 Z= 0.334 Chirality : 0.047 0.199 5107 Planarity : 0.005 0.071 5890 Dihedral : 6.137 92.407 4839 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.68 % Allowed : 16.24 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.13), residues: 4445 helix: 0.46 (0.12), residues: 1846 sheet: -0.28 (0.21), residues: 571 loop : -1.81 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 476 HIS 0.008 0.001 HIS F 735 PHE 0.035 0.002 PHE E 674 TYR 0.016 0.002 TYR D 244 ARG 0.009 0.001 ARG C 753 Details of bonding type rmsd hydrogen bonds : bond 0.05327 ( 1376) hydrogen bonds : angle 4.84075 ( 3867) covalent geometry : bond 0.00443 (32320) covalent geometry : angle 0.66242 (43925) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 354 time to evaluate : 3.358 Fit side-chains REVERT: A 243 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8539 (mt) REVERT: A 508 MET cc_start: 0.6663 (tpp) cc_final: 0.6385 (tpp) REVERT: B 273 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7469 (mt-10) REVERT: B 486 LYS cc_start: 0.6875 (mttt) cc_final: 0.6674 (ttpp) REVERT: B 639 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8080 (mt) REVERT: C 445 LEU cc_start: 0.6844 (tp) cc_final: 0.6526 (mt) REVERT: C 465 ARG cc_start: 0.6904 (mmp80) cc_final: 0.6335 (ptm-80) REVERT: C 531 ILE cc_start: 0.8829 (mt) cc_final: 0.8624 (mt) REVERT: C 534 GLU cc_start: 0.6502 (tm-30) cc_final: 0.6029 (tm-30) REVERT: C 564 ASP cc_start: 0.7268 (m-30) cc_final: 0.7056 (m-30) REVERT: C 568 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6878 (mt0) REVERT: C 720 MET cc_start: 0.3258 (tpt) cc_final: 0.2915 (tpt) REVERT: C 762 LEU cc_start: 0.3950 (OUTLIER) cc_final: 0.3664 (mt) REVERT: D 389 LYS cc_start: 0.7396 (tptp) cc_final: 0.6722 (mtmt) REVERT: D 424 ARG cc_start: 0.5807 (OUTLIER) cc_final: 0.5501 (ptp-110) REVERT: D 449 MET cc_start: 0.7103 (tpt) cc_final: 0.6838 (tpt) REVERT: D 464 LEU cc_start: 0.7852 (tm) cc_final: 0.7370 (tm) REVERT: D 465 ARG cc_start: 0.6528 (mmp80) cc_final: 0.5916 (ttm170) REVERT: D 745 ARG cc_start: 0.6252 (mtp-110) cc_final: 0.5651 (mtp180) REVERT: E 402 GLU cc_start: 0.7136 (pt0) cc_final: 0.6748 (pt0) REVERT: E 460 ASN cc_start: 0.6459 (t0) cc_final: 0.6022 (t0) REVERT: F 542 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8297 (mp) REVERT: F 641 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7760 (mp10) REVERT: F 657 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7350 (mm) outliers start: 103 outliers final: 63 residues processed: 427 average time/residue: 0.4491 time to fit residues: 303.0110 Evaluate side-chains 376 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 305 time to evaluate : 5.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 312 LYS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 599 ARG Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 641 GLN Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 703 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 90 optimal weight: 20.0000 chunk 432 optimal weight: 6.9990 chunk 420 optimal weight: 5.9990 chunk 399 optimal weight: 4.9990 chunk 234 optimal weight: 50.0000 chunk 196 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 259 optimal weight: 10.0000 chunk 218 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS C 490 GLN C 536 GLN D 382 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.174431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140785 restraints weight = 43595.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141415 restraints weight = 71543.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142631 restraints weight = 55966.355| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 32320 Z= 0.209 Angle : 0.705 15.463 43925 Z= 0.354 Chirality : 0.049 0.202 5107 Planarity : 0.005 0.078 5890 Dihedral : 6.261 92.937 4839 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 5.11 % Allowed : 17.39 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.12), residues: 4445 helix: 0.35 (0.12), residues: 1824 sheet: -0.35 (0.21), residues: 550 loop : -1.87 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 476 HIS 0.011 0.002 HIS F 735 PHE 0.017 0.002 PHE E 265 TYR 0.019 0.002 TYR D 244 ARG 0.011 0.001 ARG C 753 Details of bonding type rmsd hydrogen bonds : bond 0.05441 ( 1376) hydrogen bonds : angle 4.79251 ( 3867) covalent geometry : bond 0.00507 (32320) covalent geometry : angle 0.70514 (43925) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 350 time to evaluate : 3.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 MET cc_start: 0.6246 (mpp) cc_final: 0.5026 (ttm) REVERT: A 734 ASP cc_start: 0.6371 (OUTLIER) cc_final: 0.4836 (t70) REVERT: B 390 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7596 (mt) REVERT: B 486 LYS cc_start: 0.7029 (mttt) cc_final: 0.6674 (ttpp) REVERT: B 639 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8149 (mt) REVERT: B 680 ASN cc_start: 0.6920 (t0) cc_final: 0.5498 (p0) REVERT: C 465 ARG cc_start: 0.7032 (mmp80) cc_final: 0.6486 (ptm-80) REVERT: C 534 GLU cc_start: 0.6612 (tm-30) cc_final: 0.6287 (tm-30) REVERT: C 568 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6958 (mt0) REVERT: C 661 LEU cc_start: 0.7248 (mm) cc_final: 0.6922 (mt) REVERT: C 720 MET cc_start: 0.3516 (tpt) cc_final: 0.3112 (tpt) REVERT: C 723 GLU cc_start: 0.0330 (OUTLIER) cc_final: -0.0095 (tt0) REVERT: C 744 ARG cc_start: 0.5973 (OUTLIER) cc_final: 0.4738 (ptm160) REVERT: C 762 LEU cc_start: 0.4199 (OUTLIER) cc_final: 0.3829 (mt) REVERT: D 283 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: D 336 LYS cc_start: 0.7181 (mmtt) cc_final: 0.6774 (mmtm) REVERT: D 389 LYS cc_start: 0.7493 (tptp) cc_final: 0.6959 (mtmt) REVERT: D 449 MET cc_start: 0.7116 (tpt) cc_final: 0.6844 (tpt) REVERT: D 464 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7434 (tm) REVERT: D 465 ARG cc_start: 0.6755 (mmp80) cc_final: 0.5922 (ttm170) REVERT: E 402 GLU cc_start: 0.7071 (pt0) cc_final: 0.6785 (pt0) REVERT: E 460 ASN cc_start: 0.6331 (t0) cc_final: 0.6010 (t0) REVERT: E 614 LYS cc_start: 0.6720 (mmmt) cc_final: 0.6502 (mmtt) REVERT: E 666 VAL cc_start: 0.8004 (OUTLIER) cc_final: 0.7781 (p) REVERT: F 252 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8430 (m) REVERT: F 459 SER cc_start: 0.6736 (OUTLIER) cc_final: 0.6419 (m) REVERT: F 479 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7760 (mm) REVERT: F 542 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8271 (mp) REVERT: F 578 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7147 (mt-10) REVERT: F 641 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: F 657 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7317 (mm) outliers start: 143 outliers final: 77 residues processed: 458 average time/residue: 0.5567 time to fit residues: 405.7498 Evaluate side-chains 401 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 307 time to evaluate : 4.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 744 ARG Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 599 ARG Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 641 GLN Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 703 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 240 optimal weight: 1.9990 chunk 251 optimal weight: 8.9990 chunk 252 optimal weight: 0.9990 chunk 390 optimal weight: 8.9990 chunk 360 optimal weight: 0.8980 chunk 273 optimal weight: 8.9990 chunk 358 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 chunk 142 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN C 340 HIS C 490 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 ASN E 714 GLN F 317 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.176096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142279 restraints weight = 43262.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139861 restraints weight = 66642.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.142220 restraints weight = 59981.808| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32320 Z= 0.143 Angle : 0.613 10.199 43925 Z= 0.305 Chirality : 0.045 0.157 5107 Planarity : 0.004 0.076 5890 Dihedral : 5.939 92.962 4839 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.18 % Allowed : 19.56 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 4445 helix: 0.58 (0.12), residues: 1826 sheet: -0.27 (0.22), residues: 549 loop : -1.77 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 454 HIS 0.005 0.001 HIS F 735 PHE 0.025 0.001 PHE E 674 TYR 0.017 0.002 TYR D 244 ARG 0.012 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 1376) hydrogen bonds : angle 4.53963 ( 3867) covalent geometry : bond 0.00337 (32320) covalent geometry : angle 0.61297 (43925) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8890 Ramachandran restraints generated. 4445 Oldfield, 0 Emsley, 4445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 338 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.8065 (pm20) cc_final: 0.7864 (pm20) REVERT: A 678 MET cc_start: 0.6164 (mpp) cc_final: 0.4962 (ttm) REVERT: B 639 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8100 (mt) REVERT: B 680 ASN cc_start: 0.6919 (t0) cc_final: 0.5474 (p0) REVERT: B 713 ARG cc_start: 0.5012 (OUTLIER) cc_final: 0.4233 (ptm-80) REVERT: C 426 LYS cc_start: 0.6661 (mmmm) cc_final: 0.6358 (mtmt) REVERT: C 465 ARG cc_start: 0.7081 (mmp80) cc_final: 0.6396 (ptm-80) REVERT: C 508 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6909 (tmt) REVERT: C 534 GLU cc_start: 0.6517 (tm-30) cc_final: 0.6220 (tm-30) REVERT: C 568 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6822 (mt0) REVERT: C 723 GLU cc_start: 0.0578 (OUTLIER) cc_final: 0.0105 (tt0) REVERT: D 283 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: D 336 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6748 (mmtm) REVERT: D 449 MET cc_start: 0.7110 (tpt) cc_final: 0.6799 (tpt) REVERT: D 464 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7202 (tm) REVERT: D 465 ARG cc_start: 0.6721 (mmp80) cc_final: 0.5928 (ttm170) REVERT: E 332 MET cc_start: 0.8839 (mmm) cc_final: 0.8073 (tpt) REVERT: E 402 GLU cc_start: 0.7050 (pt0) cc_final: 0.6761 (pt0) REVERT: E 460 ASN cc_start: 0.6273 (t0) cc_final: 0.5979 (t0) REVERT: F 283 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6378 (mt-10) REVERT: F 479 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7688 (mm) REVERT: F 534 GLU cc_start: 0.7104 (tt0) cc_final: 0.6899 (tt0) REVERT: F 542 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8248 (mp) REVERT: F 641 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7638 (mp10) REVERT: F 657 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7229 (mm) outliers start: 117 outliers final: 75 residues processed: 422 average time/residue: 0.4365 time to fit residues: 293.9395 Evaluate side-chains 402 residues out of total 3797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 315 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 751 ASP Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 713 ARG Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 699 ILE Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 312 LYS Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 599 ARG Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 641 GLN Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 703 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.0934 > 50: distance: 49 - 68: 11.693 distance: 54 - 76: 21.396 distance: 57 - 60: 6.079 distance: 58 - 81: 31.145 distance: 60 - 61: 3.472 distance: 61 - 62: 9.747 distance: 61 - 64: 11.562 distance: 62 - 63: 14.572 distance: 62 - 68: 6.474 distance: 63 - 86: 28.954 distance: 64 - 65: 8.283 distance: 65 - 66: 11.107 distance: 65 - 67: 5.998 distance: 68 - 69: 13.322 distance: 69 - 70: 13.596 distance: 69 - 72: 9.814 distance: 70 - 71: 5.211 distance: 70 - 76: 7.710 distance: 71 - 94: 24.217 distance: 72 - 73: 7.891 distance: 73 - 74: 17.530 distance: 73 - 75: 15.097 distance: 76 - 77: 6.568 distance: 77 - 78: 12.046 distance: 77 - 80: 12.369 distance: 78 - 79: 32.127 distance: 78 - 81: 20.630 distance: 79 - 100: 20.695 distance: 81 - 82: 30.298 distance: 82 - 83: 17.370 distance: 82 - 85: 29.192 distance: 83 - 84: 18.739 distance: 83 - 86: 6.832 distance: 84 - 106: 37.896 distance: 86 - 87: 4.047 distance: 87 - 88: 7.682 distance: 87 - 90: 5.256 distance: 88 - 89: 6.987 distance: 88 - 94: 12.805 distance: 89 - 115: 8.105 distance: 90 - 91: 13.483 distance: 91 - 92: 8.817 distance: 91 - 93: 16.487 distance: 94 - 95: 8.080 distance: 95 - 98: 7.422 distance: 96 - 97: 4.075 distance: 97 - 120: 16.622 distance: 98 - 99: 20.706 distance: 100 - 101: 4.317 distance: 101 - 102: 4.143 distance: 101 - 104: 15.072 distance: 102 - 103: 5.310 distance: 102 - 106: 3.635 distance: 103 - 125: 13.617 distance: 104 - 105: 14.577 distance: 106 - 107: 8.765 distance: 107 - 110: 11.577 distance: 108 - 109: 5.285 distance: 109 - 133: 13.280 distance: 110 - 111: 13.981 distance: 111 - 112: 14.380 distance: 112 - 113: 18.332 distance: 112 - 114: 16.079 distance: 116 - 117: 4.417 distance: 116 - 119: 6.303 distance: 117 - 118: 7.159 distance: 120 - 121: 9.840 distance: 121 - 122: 6.792 distance: 121 - 124: 11.565 distance: 122 - 123: 3.184 distance: 122 - 125: 3.234 distance: 123 - 143: 6.782