Starting phenix.real_space_refine on Fri Mar 6 23:18:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rl9_24522/03_2026/7rl9_24522.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rl9_24522/03_2026/7rl9_24522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rl9_24522/03_2026/7rl9_24522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rl9_24522/03_2026/7rl9_24522.map" model { file = "/net/cci-nas-00/data/ceres_data/7rl9_24522/03_2026/7rl9_24522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rl9_24522/03_2026/7rl9_24522.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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 24 5.49 5 S 180 5.16 5 C 22098 2.51 5 N 6192 2.21 5 O 6726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35220 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5816 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 703} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" 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: "B" 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: "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: 7.59, per 1000 atoms: 0.22 Number of scatterers: 35220 At special positions: 0 Unit cell: (166.402, 181.83, 115.71, 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 180 16.00 P 24 15.00 O 6726 8.00 N 6192 7.00 C 22098 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.4 seconds 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8316 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 18 sheets defined 45.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.749A pdb=" N MET A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 removed outlier: 4.038A pdb=" N VAL A 88 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.808A pdb=" N TYR A 138 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 200 removed outlier: 3.784A pdb=" N GLU A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.154A pdb=" N GLU A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.496A 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 250 through 263 Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.656A pdb=" N ILE A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.674A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 334 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.777A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.566A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 407 through 427 removed outlier: 3.757A pdb=" N ALA A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 4.360A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 443' Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.607A 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 491 removed outlier: 3.946A pdb=" N LYS A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 507 removed outlier: 4.026A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 removed outlier: 3.844A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.552A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 569 removed outlier: 3.851A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 649 through 661 removed outlier: 4.054A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.629A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 707 removed outlier: 3.513A pdb=" N GLU A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 4.435A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 749 through 764 removed outlier: 3.747A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.748A pdb=" N MET B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 removed outlier: 4.036A pdb=" N VAL B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.809A pdb=" N TYR B 138 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 removed outlier: 3.785A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.154A pdb=" N GLU B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.495A 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 250 through 263 Processing helix chain 'B' and resid 270 through 276 removed outlier: 3.657A pdb=" N ILE B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.673A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 334 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.778A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.565A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS B 384 " --> pdb=" O ILE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 407 through 427 removed outlier: 3.758A pdb=" N ALA B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 4.361A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.607A 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 491 removed outlier: 3.946A pdb=" N LYS B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 507 removed outlier: 4.025A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 removed outlier: 3.845A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.552A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 569 removed outlier: 3.851A pdb=" N ILE B 562 " --> pdb=" O ASN B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 649 through 661 removed outlier: 4.055A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.629A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 707 removed outlier: 3.512A pdb=" N GLU B 689 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 4.435A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 749 through 764 removed outlier: 3.747A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR B 755 " --> pdb=" O ASP B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.749A pdb=" N MET C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 removed outlier: 4.036A pdb=" N VAL C 88 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.809A pdb=" N TYR C 138 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 200 removed outlier: 3.785A pdb=" N GLU C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 200 " --> pdb=" O GLU C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.154A pdb=" N GLU C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 270 through 276 removed outlier: 3.657A pdb=" N ILE C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.673A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 334 Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.778A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.566A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 407 through 427 removed outlier: 3.757A pdb=" N ALA C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 4.360A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.608A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 491 removed outlier: 3.947A pdb=" N LYS C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 507 removed outlier: 4.026A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 removed outlier: 3.844A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.552A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 removed outlier: 3.851A pdb=" N ILE C 562 " --> pdb=" O ASN C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 649 through 661 removed outlier: 4.053A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.629A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 707 removed outlier: 3.512A pdb=" N GLU C 689 " --> pdb=" O ALA C 685 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 removed outlier: 4.434A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 743 No H-bonds generated for 'chain 'C' and resid 741 through 743' Processing helix chain 'C' and resid 749 through 764 removed outlier: 3.747A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.748A pdb=" N MET D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 removed outlier: 4.037A pdb=" N VAL D 88 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.809A pdb=" N TYR D 138 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 200 removed outlier: 3.784A pdb=" N GLU D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.154A pdb=" N GLU D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.496A 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 250 through 263 Processing helix chain 'D' and resid 270 through 276 removed outlier: 3.657A pdb=" N ILE D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.673A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 334 Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.777A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.566A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS D 384 " --> pdb=" O ILE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'D' and resid 407 through 427 removed outlier: 3.757A pdb=" N ALA D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 424 " --> pdb=" O LEU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 removed outlier: 4.359A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 438 through 443' Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.607A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 491 removed outlier: 3.946A pdb=" N LYS D 486 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.026A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 removed outlier: 3.844A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.552A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 569 removed outlier: 3.852A pdb=" N ILE D 562 " --> pdb=" O ASN D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 649 through 661 removed outlier: 4.053A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.629A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 707 removed outlier: 3.511A pdb=" N GLU D 689 " --> pdb=" O ALA D 685 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE D 707 " --> pdb=" O ILE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 4.435A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 749 through 764 removed outlier: 3.747A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D 755 " --> pdb=" O ASP D 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 removed outlier: 3.748A pdb=" N MET E 46 " --> pdb=" O SER E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 90 removed outlier: 4.037A pdb=" N VAL E 88 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 139 removed outlier: 3.809A pdb=" N TYR E 138 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 removed outlier: 3.785A pdb=" N GLU E 194 " --> pdb=" O LYS E 190 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU E 200 " --> pdb=" O GLU E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.154A pdb=" N GLU E 218 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET E 219 " --> pdb=" O GLN E 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 270 through 276 removed outlier: 3.657A pdb=" N ILE E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.673A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 334 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.777A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 removed outlier: 3.566A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS E 384 " --> pdb=" O ILE E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 403 Processing helix chain 'E' and resid 407 through 427 removed outlier: 3.757A pdb=" N ALA E 412 " --> pdb=" O GLY E 408 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 422 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG E 424 " --> pdb=" O LEU E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 removed outlier: 4.360A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 438 through 443' Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.608A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 491 removed outlier: 3.946A pdb=" N LYS E 486 " --> pdb=" O LEU E 482 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 507 removed outlier: 4.026A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 removed outlier: 3.844A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.551A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 569 removed outlier: 3.852A pdb=" N ILE E 562 " --> pdb=" O ASN E 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 634 Processing helix chain 'E' and resid 649 through 661 removed outlier: 4.055A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.629A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 707 removed outlier: 3.512A pdb=" N GLU E 689 " --> pdb=" O ALA E 685 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE E 707 " --> pdb=" O ILE E 703 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 4.435A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 749 through 764 removed outlier: 3.748A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR E 755 " --> pdb=" O ASP E 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.749A pdb=" N MET F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 90 removed outlier: 4.036A pdb=" N VAL F 88 " --> pdb=" O ASN F 85 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG F 89 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 139 removed outlier: 3.809A pdb=" N TYR F 138 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 200 removed outlier: 3.784A pdb=" N GLU F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU F 200 " --> pdb=" O GLU F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.154A pdb=" N GLU F 218 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET F 219 " --> pdb=" O GLN F 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 270 through 276 removed outlier: 3.657A pdb=" N ILE F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.674A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 334 Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.778A pdb=" N ARG F 359 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 removed outlier: 3.565A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS F 384 " --> pdb=" O ILE F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 403 Processing helix chain 'F' and resid 407 through 427 removed outlier: 3.757A pdb=" N ALA F 412 " --> pdb=" O GLY F 408 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG F 424 " --> pdb=" O LEU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 removed outlier: 4.360A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 438 through 443' Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.607A 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 491 removed outlier: 3.945A pdb=" N LYS F 486 " --> pdb=" O LEU F 482 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 499 through 507 removed outlier: 4.026A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 removed outlier: 3.845A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.551A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 569 removed outlier: 3.851A pdb=" N ILE F 562 " --> pdb=" O ASN F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 634 Processing helix chain 'F' and resid 649 through 661 removed outlier: 4.055A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.629A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 707 removed outlier: 3.511A pdb=" N GLU F 689 " --> pdb=" O ALA F 685 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE F 707 " --> pdb=" O ILE F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 740 removed outlier: 4.434A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 743 No H-bonds generated for 'chain 'F' and resid 741 through 743' Processing helix chain 'F' and resid 749 through 764 removed outlier: 3.747A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR F 755 " --> pdb=" O ASP F 751 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 60 removed outlier: 3.824A pdb=" N LEU A 58 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 103 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 269 removed outlier: 5.903A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.431A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.825A pdb=" N LEU B 58 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 103 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 265 through 269 removed outlier: 5.904A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 241 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.430A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.824A pdb=" N LEU C 58 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 103 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 265 through 269 removed outlier: 5.905A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE C 241 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.430A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.824A pdb=" N LEU D 58 " --> pdb=" O GLN D 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D 103 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 265 through 269 removed outlier: 5.903A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE D 241 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.431A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.824A pdb=" N LEU E 58 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 103 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 265 through 269 removed outlier: 5.904A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE E 241 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.430A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 58 through 60 removed outlier: 3.825A pdb=" N LEU F 58 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 265 through 269 removed outlier: 5.904A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE F 241 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.430A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1026 hydrogen bonds defined for protein. 2880 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: 7.22 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12013 1.34 - 1.46: 5005 1.46 - 1.58: 18484 1.58 - 1.69: 30 1.69 - 1.81: 288 Bond restraints: 35820 Sorted by residual: bond pdb=" C4 ADP B1002 " pdb=" C5 ADP B1002 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.86e+00 bond pdb=" C4 ADP D1002 " pdb=" C5 ADP D1002 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" C4 ADP E1002 " pdb=" C5 ADP E1002 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.80e+00 bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.80e+00 bond pdb=" C4 ADP A1002 " pdb=" C5 ADP A1002 " ideal model delta sigma weight residual 1.490 1.446 0.044 2.00e-02 2.50e+03 4.76e+00 ... (remaining 35815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 47255 2.12 - 4.23: 942 4.23 - 6.35: 197 6.35 - 8.46: 26 8.46 - 10.58: 12 Bond angle restraints: 48432 Sorted by residual: angle pdb=" N ILE C 32 " pdb=" CA ILE C 32 " pdb=" C ILE C 32 " ideal model delta sigma weight residual 113.71 108.56 5.15 9.50e-01 1.11e+00 2.94e+01 angle pdb=" N ILE A 32 " pdb=" CA ILE A 32 " pdb=" C ILE A 32 " ideal model delta sigma weight residual 113.71 108.58 5.13 9.50e-01 1.11e+00 2.92e+01 angle pdb=" N ILE E 32 " pdb=" CA ILE E 32 " pdb=" C ILE E 32 " ideal model delta sigma weight residual 113.71 108.60 5.11 9.50e-01 1.11e+00 2.90e+01 angle pdb=" N ILE F 32 " pdb=" CA ILE F 32 " pdb=" C ILE F 32 " ideal model delta sigma weight residual 113.71 108.60 5.11 9.50e-01 1.11e+00 2.89e+01 angle pdb=" N ILE B 32 " pdb=" CA ILE B 32 " pdb=" C ILE B 32 " ideal model delta sigma weight residual 113.71 108.62 5.09 9.50e-01 1.11e+00 2.87e+01 ... (remaining 48427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.32: 21907 33.32 - 66.63: 207 66.63 - 99.95: 14 99.95 - 133.26: 10 133.26 - 166.58: 8 Dihedral angle restraints: 22146 sinusoidal: 9312 harmonic: 12834 Sorted by residual: dihedral pdb=" C5' ADP E1001 " pdb=" O5' ADP E1001 " pdb=" PA ADP E1001 " pdb=" O2A ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 106.58 -166.58 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' ADP B1001 " pdb=" O5' ADP B1001 " pdb=" PA ADP B1001 " pdb=" O2A ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 106.10 -166.10 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" O2A ADP E1001 " pdb=" O3A ADP E1001 " pdb=" PA ADP E1001 " pdb=" PB ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 100.65 -160.65 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 22143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3458 0.037 - 0.074: 1465 0.074 - 0.110: 425 0.110 - 0.147: 94 0.147 - 0.184: 6 Chirality restraints: 5448 Sorted by residual: chirality pdb=" CG LEU E 420 " pdb=" CB LEU E 420 " pdb=" CD1 LEU E 420 " pdb=" CD2 LEU E 420 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CG LEU C 420 " pdb=" CB LEU C 420 " pdb=" CD1 LEU C 420 " pdb=" CD2 LEU C 420 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CG LEU D 420 " pdb=" CB LEU D 420 " pdb=" CD1 LEU D 420 " pdb=" CD2 LEU D 420 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 5445 not shown) Planarity restraints: 6354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 20 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C LYS D 20 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS D 20 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN D 21 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 20 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C LYS B 20 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS B 20 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN B 21 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 20 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.91e+00 pdb=" C LYS A 20 " -0.029 2.00e-02 2.50e+03 pdb=" O LYS A 20 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN A 21 " 0.010 2.00e-02 2.50e+03 ... (remaining 6351 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3287 2.75 - 3.29: 35141 3.29 - 3.82: 53952 3.82 - 4.36: 64439 4.36 - 4.90: 106716 Nonbonded interactions: 263535 Sorted by model distance: nonbonded pdb=" O ASP E 669 " pdb=" NH2 ARG E 733 " model vdw 2.210 3.120 nonbonded pdb=" O ASP A 669 " pdb=" NH2 ARG A 733 " model vdw 2.211 3.120 nonbonded pdb=" O ASP F 669 " pdb=" NH2 ARG F 733 " model vdw 2.211 3.120 nonbonded pdb=" O ASP D 669 " pdb=" NH2 ARG D 733 " model vdw 2.211 3.120 nonbonded pdb=" O ASP C 669 " pdb=" NH2 ARG C 733 " model vdw 2.211 3.120 ... (remaining 263530 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 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: 0.050 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.500 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.010 0.846 35828 Z= 0.989 Angle : 0.727 10.575 48432 Z= 0.392 Chirality : 0.044 0.184 5448 Planarity : 0.003 0.048 6354 Dihedral : 11.046 166.576 13830 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.13 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.13), residues: 4440 helix: -0.41 (0.13), residues: 1656 sheet: 0.68 (0.26), residues: 456 loop : -2.28 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 567 TYR 0.009 0.001 TYR A 755 PHE 0.006 0.001 PHE E 773 TRP 0.012 0.001 TRP C 454 HIS 0.002 0.001 HIS D 404 Details of bonding type rmsd covalent geometry : bond 0.00337 (35820) covalent geometry : angle 0.72725 (48432) hydrogen bonds : bond 0.27125 ( 1026) hydrogen bonds : angle 6.87952 ( 2880) Misc. bond : bond 0.65196 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.7145 (m110) cc_final: 0.6895 (m110) REVERT: B 332 MET cc_start: 0.8965 (tpp) cc_final: 0.8755 (tpp) REVERT: D 199 ASN cc_start: 0.7078 (m110) cc_final: 0.6835 (m110) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1908 time to fit residues: 64.7609 Evaluate side-chains 169 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 0.0000 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN F 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.149250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.094826 restraints weight = 74659.056| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 4.56 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 35828 Z= 0.157 Angle : 0.621 8.798 48432 Z= 0.295 Chirality : 0.045 0.166 5448 Planarity : 0.004 0.046 6354 Dihedral : 9.070 167.306 4962 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.15 % Favored : 91.58 % Rotamer: Outliers : 0.47 % Allowed : 3.85 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.13), residues: 4440 helix: -0.35 (0.12), residues: 1776 sheet: 0.91 (0.26), residues: 450 loop : -2.11 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 377 TYR 0.013 0.001 TYR C 755 PHE 0.015 0.001 PHE F 773 TRP 0.010 0.001 TRP B 454 HIS 0.004 0.001 HIS C 340 Details of bonding type rmsd covalent geometry : bond 0.00365 (35820) covalent geometry : angle 0.62137 (48432) hydrogen bonds : bond 0.04350 ( 1026) hydrogen bonds : angle 4.64375 ( 2880) Misc. bond : bond 0.00328 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.6945 (m110) cc_final: 0.6669 (m110) REVERT: A 388 MET cc_start: 0.8057 (ptt) cc_final: 0.7812 (ptt) REVERT: A 668 LYS cc_start: 0.9076 (mppt) cc_final: 0.8866 (mtmm) REVERT: B 199 ASN cc_start: 0.6872 (m110) cc_final: 0.6626 (m110) REVERT: B 454 TRP cc_start: 0.8969 (t60) cc_final: 0.8676 (t60) REVERT: C 199 ASN cc_start: 0.6937 (m110) cc_final: 0.6696 (m110) REVERT: D 199 ASN cc_start: 0.6966 (m110) cc_final: 0.6689 (m110) REVERT: E 199 ASN cc_start: 0.6845 (m110) cc_final: 0.6596 (m110) REVERT: E 454 TRP cc_start: 0.8980 (t60) cc_final: 0.8667 (t60) REVERT: F 199 ASN cc_start: 0.6919 (m110) cc_final: 0.6680 (m110) outliers start: 18 outliers final: 8 residues processed: 209 average time/residue: 0.1875 time to fit residues: 67.1777 Evaluate side-chains 193 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 300 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 105 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 229 optimal weight: 40.0000 chunk 265 optimal weight: 3.9990 chunk 232 optimal weight: 30.0000 chunk 300 optimal weight: 0.0270 chunk 441 optimal weight: 0.0980 chunk 138 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 ASN E 494 GLN F 351 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.148508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094824 restraints weight = 74050.651| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 4.45 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35828 Z= 0.112 Angle : 0.560 10.162 48432 Z= 0.259 Chirality : 0.044 0.166 5448 Planarity : 0.003 0.043 6354 Dihedral : 8.661 173.820 4962 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.55 % Favored : 92.32 % Rotamer: Outliers : 0.69 % Allowed : 5.06 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.13), residues: 4440 helix: 0.05 (0.12), residues: 1782 sheet: 1.02 (0.26), residues: 450 loop : -1.91 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 377 TYR 0.013 0.001 TYR A 755 PHE 0.010 0.001 PHE F 290 TRP 0.007 0.001 TRP F 454 HIS 0.003 0.001 HIS F 340 Details of bonding type rmsd covalent geometry : bond 0.00261 (35820) covalent geometry : angle 0.56050 (48432) hydrogen bonds : bond 0.03499 ( 1026) hydrogen bonds : angle 4.17821 ( 2880) Misc. bond : bond 0.00141 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.6978 (m110) cc_final: 0.6682 (m110) REVERT: A 344 MET cc_start: 0.8886 (mtp) cc_final: 0.8682 (mtp) REVERT: B 199 ASN cc_start: 0.6801 (m110) cc_final: 0.6538 (m110) REVERT: C 199 ASN cc_start: 0.6997 (m110) cc_final: 0.6764 (m110) REVERT: D 199 ASN cc_start: 0.6888 (m110) cc_final: 0.6609 (m110) REVERT: E 199 ASN cc_start: 0.6772 (m110) cc_final: 0.6507 (m110) REVERT: E 332 MET cc_start: 0.8830 (mmm) cc_final: 0.8553 (tpt) REVERT: F 199 ASN cc_start: 0.6970 (m110) cc_final: 0.6741 (m110) REVERT: F 668 LYS cc_start: 0.9189 (mppt) cc_final: 0.8953 (mppt) outliers start: 26 outliers final: 16 residues processed: 213 average time/residue: 0.1709 time to fit residues: 63.9535 Evaluate side-chains 195 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 689 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 303 optimal weight: 9.9990 chunk 334 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 418 optimal weight: 0.0670 chunk 245 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 chunk 77 optimal weight: 50.0000 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 348 ASN A 616 ASN B 384 HIS B 616 ASN C 348 ASN C 616 ASN D 285 ASN D 348 ASN D 616 ASN E 384 HIS F 351 ASN F 616 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.145967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089638 restraints weight = 70992.922| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.82 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35828 Z= 0.129 Angle : 0.562 8.233 48432 Z= 0.260 Chirality : 0.044 0.164 5448 Planarity : 0.003 0.044 6354 Dihedral : 8.131 167.178 4962 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.95 % Favored : 91.91 % Rotamer: Outliers : 0.82 % Allowed : 5.93 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.13), residues: 4440 helix: 0.34 (0.13), residues: 1764 sheet: 1.09 (0.26), residues: 450 loop : -1.87 (0.14), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 766 TYR 0.009 0.001 TYR F 755 PHE 0.014 0.001 PHE A 768 TRP 0.008 0.001 TRP B 454 HIS 0.003 0.001 HIS F 340 Details of bonding type rmsd covalent geometry : bond 0.00305 (35820) covalent geometry : angle 0.56186 (48432) hydrogen bonds : bond 0.02950 ( 1026) hydrogen bonds : angle 4.05568 ( 2880) Misc. bond : bond 0.00155 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.7103 (m110) cc_final: 0.6784 (m110) REVERT: A 344 MET cc_start: 0.9023 (mtp) cc_final: 0.8780 (mtp) REVERT: B 199 ASN cc_start: 0.6889 (m110) cc_final: 0.6614 (m110) REVERT: C 199 ASN cc_start: 0.6982 (m110) cc_final: 0.6707 (m110) REVERT: D 199 ASN cc_start: 0.7066 (m110) cc_final: 0.6754 (m110) REVERT: E 199 ASN cc_start: 0.6822 (m110) cc_final: 0.6533 (m110) REVERT: F 199 ASN cc_start: 0.6956 (m110) cc_final: 0.6681 (m110) outliers start: 31 outliers final: 26 residues processed: 212 average time/residue: 0.1812 time to fit residues: 67.1134 Evaluate side-chains 201 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 171 optimal weight: 0.3980 chunk 162 optimal weight: 8.9990 chunk 213 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 328 optimal weight: 4.9990 chunk 380 optimal weight: 0.0000 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN B 285 ASN B 348 ASN C 285 ASN C 351 ASN C 494 GLN E 285 ASN E 348 ASN E 616 ASN F 285 ASN F 494 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.147903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.091545 restraints weight = 68870.979| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 5.82 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35828 Z= 0.108 Angle : 0.545 7.159 48432 Z= 0.249 Chirality : 0.044 0.148 5448 Planarity : 0.003 0.044 6354 Dihedral : 7.302 168.594 4962 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.21 % Favored : 92.66 % Rotamer: Outliers : 1.40 % Allowed : 6.07 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.13), residues: 4440 helix: 0.56 (0.13), residues: 1734 sheet: 1.22 (0.26), residues: 450 loop : -1.75 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 560 TYR 0.010 0.001 TYR A 244 PHE 0.011 0.001 PHE F 290 TRP 0.007 0.001 TRP E 454 HIS 0.003 0.001 HIS C 340 Details of bonding type rmsd covalent geometry : bond 0.00255 (35820) covalent geometry : angle 0.54454 (48432) hydrogen bonds : bond 0.02752 ( 1026) hydrogen bonds : angle 3.94325 ( 2880) Misc. bond : bond 0.00114 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 187 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.7003 (m110) cc_final: 0.6664 (m110) REVERT: B 199 ASN cc_start: 0.6986 (m110) cc_final: 0.6671 (m110) REVERT: B 497 VAL cc_start: 0.9463 (OUTLIER) cc_final: 0.9232 (m) REVERT: C 199 ASN cc_start: 0.7060 (m110) cc_final: 0.6744 (m110) REVERT: C 740 MET cc_start: 0.9507 (tpt) cc_final: 0.9241 (mmm) REVERT: D 199 ASN cc_start: 0.6907 (m110) cc_final: 0.6574 (m110) REVERT: D 497 VAL cc_start: 0.9470 (OUTLIER) cc_final: 0.9241 (m) REVERT: E 199 ASN cc_start: 0.6993 (m110) cc_final: 0.6697 (m110) REVERT: F 199 ASN cc_start: 0.6958 (m110) cc_final: 0.6660 (m110) outliers start: 53 outliers final: 28 residues processed: 227 average time/residue: 0.1828 time to fit residues: 71.7575 Evaluate side-chains 200 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 43 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 378 optimal weight: 0.0670 chunk 189 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 214 optimal weight: 0.6980 chunk 322 optimal weight: 3.9990 chunk 350 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 HIS C 406 HIS E 406 HIS F 406 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.148397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.088831 restraints weight = 67905.478| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 5.37 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35828 Z= 0.141 Angle : 0.566 9.108 48432 Z= 0.262 Chirality : 0.044 0.164 5448 Planarity : 0.003 0.044 6354 Dihedral : 6.858 169.494 4962 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.57 % Favored : 92.30 % Rotamer: Outliers : 1.50 % Allowed : 6.51 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 4440 helix: 0.66 (0.13), residues: 1740 sheet: 1.22 (0.26), residues: 450 loop : -1.70 (0.14), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 349 TYR 0.014 0.001 TYR C 244 PHE 0.012 0.001 PHE C 290 TRP 0.007 0.001 TRP C 454 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00334 (35820) covalent geometry : angle 0.56646 (48432) hydrogen bonds : bond 0.02871 ( 1026) hydrogen bonds : angle 3.96991 ( 2880) Misc. bond : bond 0.00124 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 175 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.7222 (m110) cc_final: 0.6862 (m110) REVERT: C 199 ASN cc_start: 0.7275 (m110) cc_final: 0.6885 (m110) REVERT: C 420 LEU cc_start: 0.9345 (mt) cc_final: 0.9028 (tp) REVERT: C 740 MET cc_start: 0.9650 (tpt) cc_final: 0.9351 (mmm) REVERT: D 199 ASN cc_start: 0.7195 (m110) cc_final: 0.6828 (m110) REVERT: F 199 ASN cc_start: 0.7229 (m110) cc_final: 0.6849 (m110) REVERT: F 420 LEU cc_start: 0.9377 (mt) cc_final: 0.9002 (tp) outliers start: 57 outliers final: 44 residues processed: 212 average time/residue: 0.1697 time to fit residues: 63.4157 Evaluate side-chains 208 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain F residue 731 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 117 optimal weight: 9.9990 chunk 344 optimal weight: 0.8980 chunk 393 optimal weight: 0.3980 chunk 264 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 144 optimal weight: 0.0370 chunk 140 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 149 optimal weight: 0.0020 chunk 434 optimal weight: 1.9990 overall best weight: 0.4668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.146673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.090031 restraints weight = 70100.361| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 4.74 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 35828 Z= 0.095 Angle : 0.545 10.794 48432 Z= 0.247 Chirality : 0.044 0.166 5448 Planarity : 0.003 0.044 6354 Dihedral : 6.592 170.092 4962 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.43 % Favored : 92.43 % Rotamer: Outliers : 1.13 % Allowed : 6.96 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 4440 helix: 0.80 (0.13), residues: 1728 sheet: 1.27 (0.26), residues: 438 loop : -1.65 (0.14), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 349 TYR 0.010 0.001 TYR A 244 PHE 0.013 0.001 PHE D 363 TRP 0.007 0.001 TRP C 454 HIS 0.003 0.001 HIS F 340 Details of bonding type rmsd covalent geometry : bond 0.00226 (35820) covalent geometry : angle 0.54472 (48432) hydrogen bonds : bond 0.02572 ( 1026) hydrogen bonds : angle 3.90017 ( 2880) Misc. bond : bond 0.00075 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.7175 (m110) cc_final: 0.6780 (m110) REVERT: A 740 MET cc_start: 0.9525 (mmm) cc_final: 0.9288 (tpp) REVERT: B 449 MET cc_start: 0.8728 (tpp) cc_final: 0.8466 (mpp) REVERT: B 740 MET cc_start: 0.9590 (mmm) cc_final: 0.9354 (mmm) REVERT: C 199 ASN cc_start: 0.7166 (m110) cc_final: 0.6799 (m110) REVERT: C 420 LEU cc_start: 0.9324 (mt) cc_final: 0.9025 (tp) REVERT: C 740 MET cc_start: 0.9640 (tpt) cc_final: 0.9366 (tpp) REVERT: D 199 ASN cc_start: 0.7043 (m110) cc_final: 0.6671 (m110) REVERT: D 740 MET cc_start: 0.9528 (mmm) cc_final: 0.9304 (tpp) REVERT: E 199 ASN cc_start: 0.7081 (m110) cc_final: 0.6705 (m110) REVERT: F 199 ASN cc_start: 0.7123 (m110) cc_final: 0.6757 (m110) REVERT: F 420 LEU cc_start: 0.9304 (mt) cc_final: 0.8990 (tp) outliers start: 43 outliers final: 35 residues processed: 207 average time/residue: 0.1844 time to fit residues: 66.4589 Evaluate side-chains 202 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 171 optimal weight: 0.2980 chunk 360 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 310 optimal weight: 30.0000 chunk 254 optimal weight: 0.0040 chunk 12 optimal weight: 0.9980 chunk 407 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.144751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.087350 restraints weight = 70148.337| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 4.71 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35828 Z= 0.124 Angle : 0.552 9.137 48432 Z= 0.253 Chirality : 0.044 0.169 5448 Planarity : 0.003 0.043 6354 Dihedral : 6.541 171.147 4962 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.27 % Favored : 92.59 % Rotamer: Outliers : 1.21 % Allowed : 6.91 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.13), residues: 4440 helix: 0.87 (0.13), residues: 1734 sheet: 1.22 (0.26), residues: 456 loop : -1.61 (0.14), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 349 TYR 0.015 0.001 TYR C 244 PHE 0.011 0.001 PHE D 363 TRP 0.006 0.001 TRP C 454 HIS 0.003 0.001 HIS F 340 Details of bonding type rmsd covalent geometry : bond 0.00294 (35820) covalent geometry : angle 0.55250 (48432) hydrogen bonds : bond 0.02699 ( 1026) hydrogen bonds : angle 3.91127 ( 2880) Misc. bond : bond 0.00093 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.7330 (m110) cc_final: 0.6942 (m110) REVERT: A 740 MET cc_start: 0.9543 (mmm) cc_final: 0.9314 (tpp) REVERT: B 740 MET cc_start: 0.9574 (mmm) cc_final: 0.9322 (mmm) REVERT: C 199 ASN cc_start: 0.7296 (m110) cc_final: 0.6890 (m110) REVERT: C 420 LEU cc_start: 0.9302 (mt) cc_final: 0.9015 (tp) REVERT: C 740 MET cc_start: 0.9696 (tpt) cc_final: 0.9469 (tpp) REVERT: D 740 MET cc_start: 0.9536 (mmm) cc_final: 0.9326 (tpp) REVERT: F 199 ASN cc_start: 0.7272 (m110) cc_final: 0.6878 (m110) REVERT: F 420 LEU cc_start: 0.9281 (mt) cc_final: 0.8983 (tp) outliers start: 46 outliers final: 39 residues processed: 194 average time/residue: 0.1841 time to fit residues: 61.8908 Evaluate side-chains 198 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 731 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 170 optimal weight: 0.0980 chunk 128 optimal weight: 0.6980 chunk 139 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 225 optimal weight: 40.0000 chunk 89 optimal weight: 10.0000 chunk 359 optimal weight: 3.9990 chunk 277 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.143882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.087308 restraints weight = 70846.790| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.51 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35828 Z= 0.137 Angle : 0.562 8.225 48432 Z= 0.258 Chirality : 0.044 0.176 5448 Planarity : 0.003 0.044 6354 Dihedral : 6.553 170.946 4962 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.94 % Favored : 92.93 % Rotamer: Outliers : 1.05 % Allowed : 7.25 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.13), residues: 4440 helix: 0.88 (0.13), residues: 1728 sheet: 1.23 (0.26), residues: 456 loop : -1.58 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 349 TYR 0.021 0.001 TYR B 244 PHE 0.015 0.001 PHE C 363 TRP 0.007 0.001 TRP C 454 HIS 0.003 0.001 HIS F 340 Details of bonding type rmsd covalent geometry : bond 0.00325 (35820) covalent geometry : angle 0.56173 (48432) hydrogen bonds : bond 0.02754 ( 1026) hydrogen bonds : angle 3.95893 ( 2880) Misc. bond : bond 0.00093 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 199 ASN cc_start: 0.7360 (m110) cc_final: 0.6931 (m110) REVERT: A 740 MET cc_start: 0.9561 (mmm) cc_final: 0.9282 (tpp) REVERT: B 740 MET cc_start: 0.9583 (mmm) cc_final: 0.9333 (mmm) REVERT: C 199 ASN cc_start: 0.7290 (m110) cc_final: 0.6881 (m110) REVERT: C 420 LEU cc_start: 0.9345 (mt) cc_final: 0.9038 (tp) REVERT: C 740 MET cc_start: 0.9708 (tpt) cc_final: 0.9499 (tpp) REVERT: D 740 MET cc_start: 0.9574 (mmm) cc_final: 0.9317 (tpp) REVERT: F 199 ASN cc_start: 0.7279 (m110) cc_final: 0.6898 (m110) REVERT: F 420 LEU cc_start: 0.9312 (mt) cc_final: 0.9005 (tp) outliers start: 40 outliers final: 34 residues processed: 197 average time/residue: 0.1753 time to fit residues: 61.8225 Evaluate side-chains 195 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 731 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 356 optimal weight: 3.9990 chunk 359 optimal weight: 0.9990 chunk 357 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 406 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 441 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 chunk 317 optimal weight: 0.8980 chunk 244 optimal weight: 0.0670 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.144560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.087489 restraints weight = 71134.307| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 4.74 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35828 Z= 0.108 Angle : 0.551 9.800 48432 Z= 0.252 Chirality : 0.044 0.173 5448 Planarity : 0.003 0.044 6354 Dihedral : 6.431 171.241 4962 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.60 % Favored : 93.27 % Rotamer: Outliers : 0.92 % Allowed : 7.54 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 4440 helix: 0.95 (0.13), residues: 1722 sheet: 1.22 (0.25), residues: 456 loop : -1.57 (0.14), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 349 TYR 0.017 0.001 TYR E 244 PHE 0.012 0.001 PHE C 363 TRP 0.007 0.001 TRP C 454 HIS 0.003 0.001 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00257 (35820) covalent geometry : angle 0.55097 (48432) hydrogen bonds : bond 0.02595 ( 1026) hydrogen bonds : angle 3.91310 ( 2880) Misc. bond : bond 0.00073 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 199 ASN cc_start: 0.7321 (m110) cc_final: 0.6894 (m110) REVERT: A 740 MET cc_start: 0.9549 (mmm) cc_final: 0.9322 (tpp) REVERT: B 740 MET cc_start: 0.9595 (mmm) cc_final: 0.9359 (mmm) REVERT: C 199 ASN cc_start: 0.7216 (m110) cc_final: 0.6804 (m110) REVERT: C 420 LEU cc_start: 0.9321 (mt) cc_final: 0.9035 (tp) REVERT: C 740 MET cc_start: 0.9703 (tpt) cc_final: 0.9495 (tpp) REVERT: D 740 MET cc_start: 0.9537 (mmm) cc_final: 0.9322 (tpp) REVERT: E 449 MET cc_start: 0.8793 (tpp) cc_final: 0.8293 (tpp) REVERT: F 199 ASN cc_start: 0.7198 (m110) cc_final: 0.6793 (m110) REVERT: F 420 LEU cc_start: 0.9293 (mt) cc_final: 0.8988 (tp) outliers start: 35 outliers final: 32 residues processed: 193 average time/residue: 0.1711 time to fit residues: 58.2096 Evaluate side-chains 193 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 731 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 112 optimal weight: 6.9990 chunk 224 optimal weight: 20.0000 chunk 300 optimal weight: 8.9990 chunk 211 optimal weight: 0.6980 chunk 338 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 221 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.144097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.084336 restraints weight = 69131.804| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 4.87 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35828 Z= 0.155 Angle : 0.580 10.525 48432 Z= 0.270 Chirality : 0.045 0.174 5448 Planarity : 0.003 0.044 6354 Dihedral : 6.568 170.770 4962 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.70 % Favored : 92.16 % Rotamer: Outliers : 1.05 % Allowed : 7.52 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.13), residues: 4440 helix: 0.71 (0.12), residues: 1782 sheet: 1.16 (0.25), residues: 456 loop : -1.56 (0.14), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 349 TYR 0.028 0.001 TYR E 244 PHE 0.014 0.001 PHE F 363 TRP 0.007 0.001 TRP C 454 HIS 0.003 0.001 HIS F 340 Details of bonding type rmsd covalent geometry : bond 0.00364 (35820) covalent geometry : angle 0.58009 (48432) hydrogen bonds : bond 0.02951 ( 1026) hydrogen bonds : angle 3.99893 ( 2880) Misc. bond : bond 0.00106 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6384.67 seconds wall clock time: 110 minutes 24.62 seconds (6624.62 seconds total)