Starting phenix.real_space_refine on Sat Mar 7 06:03:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vqo_32091/03_2026/7vqo_32091.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vqo_32091/03_2026/7vqo_32091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vqo_32091/03_2026/7vqo_32091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vqo_32091/03_2026/7vqo_32091.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vqo_32091/03_2026/7vqo_32091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vqo_32091/03_2026/7vqo_32091.map" } resolution = 2.19 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= 0.052 sd= 2.444 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 Zn 4 6.06 5 S 156 5.16 5 C 24156 2.51 5 N 6664 2.21 5 O 7660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 491 residue(s): 0.04s 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: 38640 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 9487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9487 Classifications: {'peptide': 1180} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 66, 'TRANS': 1113} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 9487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9487 Classifications: {'peptide': 1180} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 66, 'TRANS': 1113} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 9487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9487 Classifications: {'peptide': 1180} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 66, 'TRANS': 1113} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 9487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9487 Classifications: {'peptide': 1180} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 66, 'TRANS': 1113} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 167 Classifications: {'water': 167} Link IDs: {None: 166} Chain: "B" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "C" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "D" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Time building chain proxies: 7.99, per 1000 atoms: 0.21 Number of scatterers: 38640 At special positions: 0 Unit cell: (167.44, 142.48, 136.24, 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) Zn 4 29.99 S 156 16.00 O 7660 8.00 N 6664 7.00 C 24156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 292 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 614 " pdb=" ZN B1701 " pdb="ZN ZN B1701 " - pdb=" NE2 HIS B 292 " pdb="ZN ZN B1701 " - pdb=" NE2 HIS B 614 " pdb=" ZN C1701 " pdb="ZN ZN C1701 " - pdb=" NE2 HIS C 292 " pdb="ZN ZN C1701 " - pdb=" NE2 HIS C 614 " pdb=" ZN D1701 " pdb="ZN ZN D1701 " - pdb=" NE2 HIS D 292 " pdb="ZN ZN D1701 " - pdb=" NE2 HIS D 614 " 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8800 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 56 sheets defined 28.2% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 28 through 37 removed outlier: 3.577A pdb=" N ILE A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.738A pdb=" N MET A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.816A pdb=" N GLN A 117 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 227 Processing helix chain 'A' and resid 231 through 247 removed outlier: 4.068A pdb=" N HIS A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 removed outlier: 4.062A pdb=" N LYS A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 279 removed outlier: 3.923A pdb=" N SER A 279 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 322 removed outlier: 3.823A pdb=" N VAL A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 342 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 374 through 393 Processing helix chain 'A' and resid 411 through 419 Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 467 through 477 removed outlier: 4.024A pdb=" N MET A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 518 Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.585A pdb=" N ARG A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 544 Processing helix chain 'A' and resid 556 through 561 removed outlier: 3.549A pdb=" N TYR A 560 " --> pdb=" O ARG A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 591 removed outlier: 3.506A pdb=" N LYS A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 612 Processing helix chain 'A' and resid 622 through 651 Processing helix chain 'A' and resid 772 through 778 Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 948 through 960 removed outlier: 3.820A pdb=" N ILE A 952 " --> pdb=" O SER A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'B' and resid 28 through 37 removed outlier: 3.579A pdb=" N ILE B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 49 through 54 removed outlier: 3.738A pdb=" N MET B 53 " --> pdb=" O ASN B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.816A pdb=" N GLN B 117 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 227 Processing helix chain 'B' and resid 231 through 247 removed outlier: 4.068A pdb=" N HIS B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 removed outlier: 4.062A pdb=" N LYS B 257 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 279 removed outlier: 3.924A pdb=" N SER B 279 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 322 removed outlier: 3.824A pdb=" N VAL B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 342 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 374 through 393 Processing helix chain 'B' and resid 411 through 419 Processing helix chain 'B' and resid 427 through 432 Processing helix chain 'B' and resid 467 through 477 removed outlier: 4.024A pdb=" N MET B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 518 Processing helix chain 'B' and resid 529 through 539 removed outlier: 3.586A pdb=" N ARG B 539 " --> pdb=" O ASP B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 544 Processing helix chain 'B' and resid 556 through 561 removed outlier: 3.549A pdb=" N TYR B 560 " --> pdb=" O ARG B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 591 removed outlier: 3.505A pdb=" N LYS B 567 " --> pdb=" O GLN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 612 Processing helix chain 'B' and resid 622 through 651 Processing helix chain 'B' and resid 772 through 778 Processing helix chain 'B' and resid 873 through 878 Processing helix chain 'B' and resid 948 through 960 removed outlier: 3.820A pdb=" N ILE B 952 " --> pdb=" O SER B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 976 Processing helix chain 'C' and resid 28 through 37 removed outlier: 3.578A pdb=" N ILE C 36 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 49 through 54 removed outlier: 3.738A pdb=" N MET C 53 " --> pdb=" O ASN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.816A pdb=" N GLN C 117 " --> pdb=" O GLU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 227 Processing helix chain 'C' and resid 231 through 247 removed outlier: 4.068A pdb=" N HIS C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 268 removed outlier: 4.062A pdb=" N LYS C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 279 removed outlier: 3.923A pdb=" N SER C 279 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 322 removed outlier: 3.823A pdb=" N VAL C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER C 314 " --> pdb=" O ARG C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 342 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 374 through 393 Processing helix chain 'C' and resid 411 through 419 Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 467 through 477 removed outlier: 4.024A pdb=" N MET C 475 " --> pdb=" O VAL C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 518 Processing helix chain 'C' and resid 529 through 539 removed outlier: 3.585A pdb=" N ARG C 539 " --> pdb=" O ASP C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 544 Processing helix chain 'C' and resid 556 through 561 removed outlier: 3.549A pdb=" N TYR C 560 " --> pdb=" O ARG C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 591 removed outlier: 3.505A pdb=" N LYS C 567 " --> pdb=" O GLN C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 612 Processing helix chain 'C' and resid 622 through 651 Processing helix chain 'C' and resid 772 through 778 Processing helix chain 'C' and resid 873 through 878 Processing helix chain 'C' and resid 948 through 960 removed outlier: 3.820A pdb=" N ILE C 952 " --> pdb=" O SER C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 976 Processing helix chain 'D' and resid 28 through 37 removed outlier: 3.579A pdb=" N ILE D 36 " --> pdb=" O TYR D 32 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 49 through 54 removed outlier: 3.738A pdb=" N MET D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 113 through 117 removed outlier: 3.816A pdb=" N GLN D 117 " --> pdb=" O GLU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 227 Processing helix chain 'D' and resid 231 through 247 removed outlier: 4.069A pdb=" N HIS D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 268 removed outlier: 4.062A pdb=" N LYS D 257 " --> pdb=" O ARG D 253 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 279 removed outlier: 3.924A pdb=" N SER D 279 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 322 removed outlier: 3.824A pdb=" N VAL D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER D 314 " --> pdb=" O ARG D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 342 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 374 through 393 Processing helix chain 'D' and resid 411 through 419 Processing helix chain 'D' and resid 427 through 432 Processing helix chain 'D' and resid 467 through 477 removed outlier: 4.024A pdb=" N MET D 475 " --> pdb=" O VAL D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 518 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.586A pdb=" N ARG D 539 " --> pdb=" O ASP D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 544 Processing helix chain 'D' and resid 556 through 561 removed outlier: 3.550A pdb=" N TYR D 560 " --> pdb=" O ARG D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 591 removed outlier: 3.505A pdb=" N LYS D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 622 through 651 Processing helix chain 'D' and resid 772 through 778 Processing helix chain 'D' and resid 873 through 878 Processing helix chain 'D' and resid 948 through 960 removed outlier: 3.820A pdb=" N ILE D 952 " --> pdb=" O SER D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 971 through 976 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 59 removed outlier: 3.643A pdb=" N PHE A 196 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 59 removed outlier: 4.161A pdb=" N LYS A 200 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.636A pdb=" N LEU A 67 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A 131 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY A 132 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLY A 144 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 134 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL A 328 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY A 289 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR A 286 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE A 491 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE A 288 " --> pdb=" O PHE A 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL A 328 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY A 289 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 399 through 401 removed outlier: 4.658A pdb=" N VAL A 545 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 675 through 679 removed outlier: 3.614A pdb=" N LYS A 697 " --> pdb=" O HIS A 690 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU A 698 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR A 665 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS A 963 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 708 through 711 removed outlier: 3.586A pdb=" N ARG A 744 " --> pdb=" O ASP A 739 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 780 through 781 removed outlier: 6.789A pdb=" N LYS A 841 " --> pdb=" O ARG A 920 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARG A 920 " --> pdb=" O LYS A 841 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 843 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY A 906 " --> pdb=" O SER A 917 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 788 through 793 removed outlier: 6.427A pdb=" N SER A 798 " --> pdb=" O HIS A 790 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN A 792 " --> pdb=" O ARG A 796 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG A 796 " --> pdb=" O ASN A 792 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER A 809 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TRP A 887 " --> pdb=" O GLU A 859 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N SER A 891 " --> pdb=" O GLU A 855 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A 855 " --> pdb=" O SER A 891 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 863 " --> pdb=" O THR A 860 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 980 through 982 Processing sheet with id=AB3, first strand: chain 'A' and resid 990 through 997 removed outlier: 5.177A pdb=" N LEU A 992 " --> pdb=" O TYR A1022 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TYR A1022 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER A1073 " --> pdb=" O LYS A1044 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS A1044 " --> pdb=" O SER A1073 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG A1075 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL A1042 " --> pdb=" O ARG A1075 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A1077 " --> pdb=" O LYS A1040 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL A1042 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL A1054 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS A1044 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1125 through 1129 removed outlier: 6.896A pdb=" N VAL A1148 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP A1129 " --> pdb=" O THR A1146 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR A1146 " --> pdb=" O ASP A1129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1135 through 1137 removed outlier: 6.184A pdb=" N THR A1135 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N HIS A1235 " --> pdb=" O LEU A1225 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU A1225 " --> pdb=" O HIS A1235 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 55 through 59 removed outlier: 3.642A pdb=" N PHE B 196 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 55 through 59 removed outlier: 4.160A pdb=" N LYS B 200 " --> pdb=" O ASP B 127 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.635A pdb=" N LEU B 67 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU B 131 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY B 132 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY B 144 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 134 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL B 328 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY B 289 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR B 286 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE B 491 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE B 288 " --> pdb=" O PHE B 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL B 328 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY B 289 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 399 through 401 removed outlier: 4.658A pdb=" N VAL B 545 " --> pdb=" O THR B 441 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 675 through 679 removed outlier: 3.613A pdb=" N LYS B 697 " --> pdb=" O HIS B 690 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU B 698 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR B 665 " --> pdb=" O LEU B 698 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS B 963 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 708 through 711 removed outlier: 3.586A pdb=" N ARG B 744 " --> pdb=" O ASP B 739 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 780 through 781 removed outlier: 6.788A pdb=" N LYS B 841 " --> pdb=" O ARG B 920 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARG B 920 " --> pdb=" O LYS B 841 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 843 " --> pdb=" O LEU B 918 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLY B 906 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 788 through 793 removed outlier: 6.428A pdb=" N SER B 798 " --> pdb=" O HIS B 790 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN B 792 " --> pdb=" O ARG B 796 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG B 796 " --> pdb=" O ASN B 792 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER B 809 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TRP B 887 " --> pdb=" O GLU B 859 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER B 891 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU B 855 " --> pdb=" O SER B 891 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 863 " --> pdb=" O THR B 860 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 980 through 982 Processing sheet with id=AC8, first strand: chain 'B' and resid 990 through 997 removed outlier: 5.177A pdb=" N LEU B 992 " --> pdb=" O TYR B1022 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR B1022 " --> pdb=" O LEU B 992 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER B1073 " --> pdb=" O LYS B1044 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS B1044 " --> pdb=" O SER B1073 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG B1075 " --> pdb=" O VAL B1042 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B1042 " --> pdb=" O ARG B1075 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B1077 " --> pdb=" O LYS B1040 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL B1042 " --> pdb=" O VAL B1054 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL B1054 " --> pdb=" O VAL B1042 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS B1044 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1125 through 1129 removed outlier: 6.894A pdb=" N VAL B1148 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP B1129 " --> pdb=" O THR B1146 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR B1146 " --> pdb=" O ASP B1129 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1135 through 1137 removed outlier: 6.184A pdb=" N THR B1135 " --> pdb=" O VAL B1242 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N HIS B1235 " --> pdb=" O LEU B1225 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU B1225 " --> pdb=" O HIS B1235 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 55 through 59 removed outlier: 3.642A pdb=" N PHE C 196 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 55 through 59 removed outlier: 4.161A pdb=" N LYS C 200 " --> pdb=" O ASP C 127 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.635A pdb=" N LEU C 67 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU C 131 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY C 132 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLY C 144 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C 134 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL C 328 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY C 289 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR C 286 " --> pdb=" O LEU C 489 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE C 491 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE C 288 " --> pdb=" O PHE C 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL C 328 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY C 289 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 399 through 401 removed outlier: 4.658A pdb=" N VAL C 545 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 675 through 679 removed outlier: 3.613A pdb=" N LYS C 697 " --> pdb=" O HIS C 690 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU C 698 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR C 665 " --> pdb=" O LEU C 698 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS C 963 " --> pdb=" O LEU C 668 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 708 through 711 removed outlier: 3.586A pdb=" N ARG C 744 " --> pdb=" O ASP C 739 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 780 through 781 removed outlier: 6.788A pdb=" N LYS C 841 " --> pdb=" O ARG C 920 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARG C 920 " --> pdb=" O LYS C 841 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU C 843 " --> pdb=" O LEU C 918 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLY C 906 " --> pdb=" O SER C 917 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 788 through 793 removed outlier: 6.427A pdb=" N SER C 798 " --> pdb=" O HIS C 790 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN C 792 " --> pdb=" O ARG C 796 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG C 796 " --> pdb=" O ASN C 792 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER C 809 " --> pdb=" O VAL C 805 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TRP C 887 " --> pdb=" O GLU C 859 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER C 891 " --> pdb=" O GLU C 855 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU C 855 " --> pdb=" O SER C 891 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY C 863 " --> pdb=" O THR C 860 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 980 through 982 Processing sheet with id=AE4, first strand: chain 'C' and resid 990 through 997 removed outlier: 5.177A pdb=" N LEU C 992 " --> pdb=" O TYR C1022 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TYR C1022 " --> pdb=" O LEU C 992 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N SER C1073 " --> pdb=" O LYS C1044 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS C1044 " --> pdb=" O SER C1073 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG C1075 " --> pdb=" O VAL C1042 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL C1042 " --> pdb=" O ARG C1075 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C1077 " --> pdb=" O LYS C1040 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL C1042 " --> pdb=" O VAL C1054 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL C1054 " --> pdb=" O VAL C1042 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS C1044 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1125 through 1129 removed outlier: 6.895A pdb=" N VAL C1148 " --> pdb=" O VAL C1127 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP C1129 " --> pdb=" O THR C1146 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR C1146 " --> pdb=" O ASP C1129 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1135 through 1137 removed outlier: 6.184A pdb=" N THR C1135 " --> pdb=" O VAL C1242 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N HIS C1235 " --> pdb=" O LEU C1225 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU C1225 " --> pdb=" O HIS C1235 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 55 through 59 removed outlier: 3.642A pdb=" N PHE D 196 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 55 through 59 removed outlier: 4.160A pdb=" N LYS D 200 " --> pdb=" O ASP D 127 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.635A pdb=" N LEU D 67 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 131 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY D 132 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY D 144 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 134 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL D 328 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY D 289 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR D 286 " --> pdb=" O LEU D 489 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE D 491 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE D 288 " --> pdb=" O PHE D 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL D 328 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY D 289 " --> pdb=" O VAL D 328 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 399 through 401 removed outlier: 4.658A pdb=" N VAL D 545 " --> pdb=" O THR D 441 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 675 through 679 removed outlier: 3.613A pdb=" N LYS D 697 " --> pdb=" O HIS D 690 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU D 698 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR D 665 " --> pdb=" O LEU D 698 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS D 963 " --> pdb=" O LEU D 668 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 708 through 711 removed outlier: 3.587A pdb=" N ARG D 744 " --> pdb=" O ASP D 739 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 780 through 781 removed outlier: 6.789A pdb=" N LYS D 841 " --> pdb=" O ARG D 920 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG D 920 " --> pdb=" O LYS D 841 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU D 843 " --> pdb=" O LEU D 918 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLY D 906 " --> pdb=" O SER D 917 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 788 through 793 removed outlier: 6.427A pdb=" N SER D 798 " --> pdb=" O HIS D 790 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN D 792 " --> pdb=" O ARG D 796 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG D 796 " --> pdb=" O ASN D 792 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER D 809 " --> pdb=" O VAL D 805 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TRP D 887 " --> pdb=" O GLU D 859 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER D 891 " --> pdb=" O GLU D 855 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU D 855 " --> pdb=" O SER D 891 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 863 " --> pdb=" O THR D 860 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 980 through 982 Processing sheet with id=AF9, first strand: chain 'D' and resid 990 through 997 removed outlier: 5.177A pdb=" N LEU D 992 " --> pdb=" O TYR D1022 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR D1022 " --> pdb=" O LEU D 992 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER D1073 " --> pdb=" O LYS D1044 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS D1044 " --> pdb=" O SER D1073 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG D1075 " --> pdb=" O VAL D1042 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL D1042 " --> pdb=" O ARG D1075 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D1077 " --> pdb=" O LYS D1040 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL D1042 " --> pdb=" O VAL D1054 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL D1054 " --> pdb=" O VAL D1042 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS D1044 " --> pdb=" O LEU D1052 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 1125 through 1129 removed outlier: 6.894A pdb=" N VAL D1148 " --> pdb=" O VAL D1127 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP D1129 " --> pdb=" O THR D1146 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR D1146 " --> pdb=" O ASP D1129 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 1135 through 1137 removed outlier: 6.184A pdb=" N THR D1135 " --> pdb=" O VAL D1242 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N HIS D1235 " --> pdb=" O LEU D1225 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU D1225 " --> pdb=" O HIS D1235 " (cutoff:3.500A) 1576 hydrogen bonds defined for protein. 4368 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: 10.24 Time building geometry restraints manager: 3.93 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: 12472 1.34 - 1.46: 8737 1.46 - 1.58: 17551 1.58 - 1.70: 0 1.70 - 1.81: 240 Bond restraints: 39000 Sorted by residual: bond pdb=" CB LYS A 9 " pdb=" CG LYS A 9 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CB LYS C 9 " pdb=" CG LYS C 9 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" CB LYS D 9 " pdb=" CG LYS D 9 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" CB LYS B 9 " pdb=" CG LYS B 9 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" CB ASN B 722 " pdb=" CG ASN B 722 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.85e+00 ... (remaining 38995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 50955 1.66 - 3.32: 1629 3.32 - 4.97: 293 4.97 - 6.63: 59 6.63 - 8.29: 40 Bond angle restraints: 52976 Sorted by residual: angle pdb=" N VAL D1004 " pdb=" CA VAL D1004 " pdb=" C VAL D1004 " ideal model delta sigma weight residual 113.20 105.94 7.26 9.60e-01 1.09e+00 5.72e+01 angle pdb=" N VAL C1004 " pdb=" CA VAL C1004 " pdb=" C VAL C1004 " ideal model delta sigma weight residual 113.20 105.96 7.24 9.60e-01 1.09e+00 5.68e+01 angle pdb=" N VAL B1004 " pdb=" CA VAL B1004 " pdb=" C VAL B1004 " ideal model delta sigma weight residual 113.20 105.97 7.23 9.60e-01 1.09e+00 5.67e+01 angle pdb=" N VAL A1004 " pdb=" CA VAL A1004 " pdb=" C VAL A1004 " ideal model delta sigma weight residual 113.20 105.98 7.22 9.60e-01 1.09e+00 5.65e+01 angle pdb=" CA LYS A 9 " pdb=" CB LYS A 9 " pdb=" CG LYS A 9 " ideal model delta sigma weight residual 114.10 122.27 -8.17 2.00e+00 2.50e-01 1.67e+01 ... (remaining 52971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 19658 17.66 - 35.31: 2583 35.31 - 52.96: 630 52.96 - 70.62: 153 70.62 - 88.27: 64 Dihedral angle restraints: 23088 sinusoidal: 9428 harmonic: 13660 Sorted by residual: dihedral pdb=" CA SER A 682 " pdb=" C SER A 682 " pdb=" N GLU A 683 " pdb=" CA GLU A 683 " ideal model delta harmonic sigma weight residual 180.00 -152.79 -27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA SER D 682 " pdb=" C SER D 682 " pdb=" N GLU D 683 " pdb=" CA GLU D 683 " ideal model delta harmonic sigma weight residual -180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA SER B 682 " pdb=" C SER B 682 " pdb=" N GLU B 683 " pdb=" CA GLU B 683 " ideal model delta harmonic sigma weight residual -180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 23085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3043 0.035 - 0.070: 1692 0.070 - 0.105: 665 0.105 - 0.140: 196 0.140 - 0.176: 24 Chirality restraints: 5620 Sorted by residual: chirality pdb=" CA THR A 662 " pdb=" N THR A 662 " pdb=" C THR A 662 " pdb=" CB THR A 662 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA THR C 662 " pdb=" N THR C 662 " pdb=" C THR C 662 " pdb=" CB THR C 662 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CA THR D 662 " pdb=" N THR D 662 " pdb=" C THR D 662 " pdb=" CB THR D 662 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 5617 not shown) Planarity restraints: 6856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B1157 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO B1158 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B1158 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B1158 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A1157 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO A1158 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C1157 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO C1158 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO C1158 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C1158 " 0.035 5.00e-02 4.00e+02 ... (remaining 6853 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 466 2.47 - 3.08: 26966 3.08 - 3.69: 59778 3.69 - 4.29: 93094 4.29 - 4.90: 156663 Nonbonded interactions: 336967 Sorted by model distance: nonbonded pdb=" OD2 ASP A 404 " pdb="ZN ZN A1701 " model vdw 1.865 2.230 nonbonded pdb=" OD2 ASP C 404 " pdb="ZN ZN C1701 " model vdw 1.865 2.230 nonbonded pdb=" OD2 ASP B 404 " pdb="ZN ZN B1701 " model vdw 1.866 2.230 nonbonded pdb=" OD2 ASP D 404 " pdb="ZN ZN D1701 " model vdw 1.866 2.230 nonbonded pdb=" OD1 ASP D 294 " pdb="ZN ZN D1701 " model vdw 1.867 2.230 ... (remaining 336962 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' } 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: 0.010 Normalize map: mean=0, sd=1: 2.110 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 39.050 Find NCS groups from input model: 0.330 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:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.008 0.049 39008 Z= 0.366 Angle : 0.749 8.288 52976 Z= 0.411 Chirality : 0.049 0.176 5620 Planarity : 0.004 0.064 6856 Dihedral : 17.417 88.275 14288 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.25 % Allowed : 24.80 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.12), residues: 4696 helix: 0.91 (0.15), residues: 1176 sheet: -1.05 (0.15), residues: 1244 loop : -1.93 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 436 TYR 0.037 0.002 TYR B 895 PHE 0.020 0.002 PHE A 227 TRP 0.015 0.001 TRP A 769 HIS 0.007 0.001 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00839 (39000) covalent geometry : angle 0.74941 (52976) hydrogen bonds : bond 0.14625 ( 1560) hydrogen bonds : angle 6.37251 ( 4368) metal coordination : bond 0.00277 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 675 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8154 (ptpp) cc_final: 0.7649 (ptmt) REVERT: A 475 MET cc_start: 0.8918 (tpp) cc_final: 0.8598 (tpp) REVERT: A 600 GLU cc_start: 0.8282 (mp0) cc_final: 0.7832 (mp0) REVERT: A 680 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8326 (tptp) REVERT: A 944 GLN cc_start: 0.8294 (mt0) cc_final: 0.8072 (mt0) REVERT: B 475 MET cc_start: 0.8893 (tpp) cc_final: 0.8567 (tpp) REVERT: B 600 GLU cc_start: 0.8306 (mp0) cc_final: 0.7811 (mp0) REVERT: B 677 GLU cc_start: 0.7644 (pt0) cc_final: 0.7251 (pt0) REVERT: B 680 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8172 (tptp) REVERT: B 866 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8169 (tpp-160) REVERT: B 1053 GLU cc_start: 0.8017 (pm20) cc_final: 0.7665 (pm20) REVERT: C 475 MET cc_start: 0.8904 (tpp) cc_final: 0.8565 (tpp) REVERT: C 595 LYS cc_start: 0.8652 (tppt) cc_final: 0.8286 (ttpt) REVERT: C 677 GLU cc_start: 0.7645 (pt0) cc_final: 0.7259 (pt0) REVERT: C 680 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8232 (tptp) REVERT: C 1053 GLU cc_start: 0.7997 (pm20) cc_final: 0.7716 (pm20) REVERT: D 475 MET cc_start: 0.8866 (tpp) cc_final: 0.8527 (tpp) REVERT: D 677 GLU cc_start: 0.7665 (pt0) cc_final: 0.7385 (pt0) REVERT: D 680 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8148 (tptp) REVERT: D 866 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.8131 (tpp-160) REVERT: D 969 ASP cc_start: 0.8927 (p0) cc_final: 0.8556 (p0) REVERT: D 1053 GLU cc_start: 0.8052 (pm20) cc_final: 0.7717 (pm20) outliers start: 133 outliers final: 100 residues processed: 783 average time/residue: 0.7480 time to fit residues: 704.1016 Evaluate side-chains 751 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 647 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 807 ASP Chi-restraints excluded: chain A residue 935 HIS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 680 LYS Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 807 ASP Chi-restraints excluded: chain B residue 935 HIS Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1163 VAL Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1212 THR Chi-restraints excluded: chain B residue 1241 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 629 SER Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 680 LYS Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 807 ASP Chi-restraints excluded: chain C residue 935 HIS Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1130 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1163 VAL Chi-restraints excluded: chain C residue 1174 VAL Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1241 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 680 LYS Chi-restraints excluded: chain D residue 692 THR Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 807 ASP Chi-restraints excluded: chain D residue 935 HIS Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 1130 THR Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1174 VAL Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1241 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.7980 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 0.0370 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 470 optimal weight: 0.1980 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN A 944 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN B1059 ASN C 754 ASN C 944 GLN C1059 ASN D 754 ASN D1059 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.086065 restraints weight = 50525.865| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.70 r_work: 0.2814 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39008 Z= 0.130 Angle : 0.602 7.464 52976 Z= 0.319 Chirality : 0.044 0.150 5620 Planarity : 0.005 0.055 6856 Dihedral : 7.443 58.866 5292 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.47 % Allowed : 21.48 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.12), residues: 4696 helix: 1.13 (0.16), residues: 1200 sheet: -0.77 (0.15), residues: 1188 loop : -1.80 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 536 TYR 0.012 0.001 TYR C 626 PHE 0.017 0.001 PHE C 80 TRP 0.010 0.001 TRP D 769 HIS 0.005 0.001 HIS C 614 Details of bonding type rmsd covalent geometry : bond 0.00286 (39000) covalent geometry : angle 0.60226 (52976) hydrogen bonds : bond 0.04245 ( 1560) hydrogen bonds : angle 5.12659 ( 4368) metal coordination : bond 0.00091 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 759 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8764 (tp30) cc_final: 0.8523 (tm-30) REVERT: A 185 ASP cc_start: 0.8142 (m-30) cc_final: 0.7793 (t0) REVERT: A 227 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8349 (m-10) REVERT: A 475 MET cc_start: 0.9286 (tpp) cc_final: 0.8891 (tpp) REVERT: A 595 LYS cc_start: 0.8685 (tppt) cc_final: 0.8317 (ttpp) REVERT: A 600 GLU cc_start: 0.8490 (mp0) cc_final: 0.8006 (mp0) REVERT: A 623 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7045 (mt-10) REVERT: A 644 MET cc_start: 0.8878 (tpt) cc_final: 0.8543 (tpt) REVERT: A 680 LYS cc_start: 0.8930 (tttm) cc_final: 0.8691 (tttm) REVERT: A 833 LYS cc_start: 0.7449 (tptt) cc_final: 0.7210 (ttmm) REVERT: A 895 TYR cc_start: 0.8869 (t80) cc_final: 0.8626 (t80) REVERT: A 944 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8338 (mt0) REVERT: A 1058 GLU cc_start: 0.8658 (tp30) cc_final: 0.8452 (tp30) REVERT: B 200 LYS cc_start: 0.8329 (ptpp) cc_final: 0.7732 (ptpp) REVERT: B 227 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8378 (m-10) REVERT: B 282 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: B 475 MET cc_start: 0.9264 (tpp) cc_final: 0.8872 (tpp) REVERT: B 595 LYS cc_start: 0.8737 (tppt) cc_final: 0.8373 (ttpm) REVERT: B 600 GLU cc_start: 0.8528 (mp0) cc_final: 0.8065 (mp0) REVERT: B 677 GLU cc_start: 0.8149 (pt0) cc_final: 0.7899 (pt0) REVERT: B 680 LYS cc_start: 0.8925 (tttm) cc_final: 0.8714 (tttm) REVERT: B 711 ARG cc_start: 0.8302 (ttm110) cc_final: 0.7978 (ttm110) REVERT: B 712 GLN cc_start: 0.7828 (mm110) cc_final: 0.7517 (mm110) REVERT: B 715 LYS cc_start: 0.8966 (tptp) cc_final: 0.8746 (tppt) REVERT: B 754 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8444 (t0) REVERT: B 833 LYS cc_start: 0.7345 (tptt) cc_final: 0.7124 (ttmm) REVERT: B 1053 GLU cc_start: 0.8147 (pm20) cc_final: 0.7744 (pm20) REVERT: C 82 GLU cc_start: 0.8447 (pt0) cc_final: 0.7982 (pt0) REVERT: C 185 ASP cc_start: 0.8243 (m-30) cc_final: 0.7946 (t0) REVERT: C 200 LYS cc_start: 0.8289 (ptpp) cc_final: 0.7662 (ptpp) REVERT: C 227 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8394 (m-10) REVERT: C 475 MET cc_start: 0.9291 (tpp) cc_final: 0.8978 (tpp) REVERT: C 595 LYS cc_start: 0.8712 (tppt) cc_final: 0.8339 (ttpm) REVERT: C 600 GLU cc_start: 0.8498 (mp0) cc_final: 0.7996 (mp0) REVERT: C 680 LYS cc_start: 0.8952 (tttm) cc_final: 0.8735 (tttm) REVERT: C 711 ARG cc_start: 0.8362 (ttm110) cc_final: 0.8034 (ttm110) REVERT: C 728 HIS cc_start: 0.7074 (m-70) cc_final: 0.6053 (t-90) REVERT: C 833 LYS cc_start: 0.7297 (tptt) cc_final: 0.7081 (ttmm) REVERT: C 859 GLU cc_start: 0.8452 (tt0) cc_final: 0.8216 (tt0) REVERT: C 969 ASP cc_start: 0.8908 (p0) cc_final: 0.8585 (p0) REVERT: C 1053 GLU cc_start: 0.8114 (pm20) cc_final: 0.7733 (pm20) REVERT: C 1242 VAL cc_start: 0.8166 (t) cc_final: 0.7923 (m) REVERT: D 6 PHE cc_start: 0.8065 (t80) cc_final: 0.7478 (t80) REVERT: D 9 LYS cc_start: 0.8226 (mmpt) cc_final: 0.7740 (mmpt) REVERT: D 82 GLU cc_start: 0.8497 (pt0) cc_final: 0.8116 (pt0) REVERT: D 200 LYS cc_start: 0.8232 (ptpp) cc_final: 0.7621 (ptpp) REVERT: D 227 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8354 (m-10) REVERT: D 536 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7852 (ttp80) REVERT: D 595 LYS cc_start: 0.8758 (tppt) cc_final: 0.8403 (ttpp) REVERT: D 600 GLU cc_start: 0.8587 (mp0) cc_final: 0.8061 (mp0) REVERT: D 680 LYS cc_start: 0.8928 (tttm) cc_final: 0.8667 (tttm) REVERT: D 711 ARG cc_start: 0.8276 (ttm110) cc_final: 0.7914 (ttm110) REVERT: D 728 HIS cc_start: 0.6947 (m-70) cc_final: 0.6033 (t-90) REVERT: D 754 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8466 (t0) REVERT: D 833 LYS cc_start: 0.7438 (tptt) cc_final: 0.7207 (ttmm) REVERT: D 969 ASP cc_start: 0.8996 (p0) cc_final: 0.8698 (p0) REVERT: D 1053 GLU cc_start: 0.8158 (pm20) cc_final: 0.7790 (pm20) REVERT: D 1058 GLU cc_start: 0.8600 (tp30) cc_final: 0.7804 (tp30) outliers start: 183 outliers final: 80 residues processed: 886 average time/residue: 0.6666 time to fit residues: 723.9973 Evaluate side-chains 767 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 679 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 944 GLN Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 754 ASN Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1163 VAL Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1212 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 395 LYS Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 1000 ASP Chi-restraints excluded: chain C residue 1130 THR Chi-restraints excluded: chain C residue 1163 VAL Chi-restraints excluded: chain C residue 1174 VAL Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1219 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 754 ASN Chi-restraints excluded: chain D residue 832 SER Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1130 THR Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1174 VAL Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1219 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 216 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 357 optimal weight: 0.5980 chunk 209 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 241 optimal weight: 6.9990 chunk 189 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 439 HIS A 754 ASN A 944 GLN B 180 ASN B 439 HIS B 754 ASN C 439 HIS C 754 ASN D 439 HIS D 754 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.085901 restraints weight = 50922.436| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.69 r_work: 0.2830 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 39008 Z= 0.162 Angle : 0.599 9.724 52976 Z= 0.314 Chirality : 0.045 0.172 5620 Planarity : 0.004 0.051 6856 Dihedral : 6.460 59.428 5203 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.45 % Allowed : 21.58 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.12), residues: 4696 helix: 1.42 (0.16), residues: 1148 sheet: -0.79 (0.14), residues: 1188 loop : -1.70 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 436 TYR 0.024 0.001 TYR C1170 PHE 0.010 0.001 PHE A 80 TRP 0.010 0.001 TRP B 769 HIS 0.006 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00373 (39000) covalent geometry : angle 0.59918 (52976) hydrogen bonds : bond 0.04330 ( 1560) hydrogen bonds : angle 4.95153 ( 4368) metal coordination : bond 0.00196 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 708 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8431 (ptp90) REVERT: A 475 MET cc_start: 0.9407 (tpp) cc_final: 0.9014 (tpp) REVERT: A 600 GLU cc_start: 0.8654 (mp0) cc_final: 0.8185 (mp0) REVERT: A 680 LYS cc_start: 0.9001 (tttm) cc_final: 0.8801 (tttm) REVERT: A 711 ARG cc_start: 0.8723 (mtp85) cc_final: 0.8481 (mtp85) REVERT: A 715 LYS cc_start: 0.8914 (tptp) cc_final: 0.8397 (tppt) REVERT: A 833 LYS cc_start: 0.7717 (tptt) cc_final: 0.7455 (ttmm) REVERT: A 900 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8106 (pp) REVERT: A 1199 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7777 (mm-40) REVERT: A 1220 ILE cc_start: 0.8704 (mt) cc_final: 0.8404 (mp) REVERT: B 227 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8537 (m-10) REVERT: B 310 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8390 (ptp90) REVERT: B 475 MET cc_start: 0.9394 (tpp) cc_final: 0.9011 (tpp) REVERT: B 595 LYS cc_start: 0.8814 (tppt) cc_final: 0.8424 (ttpm) REVERT: B 600 GLU cc_start: 0.8666 (mp0) cc_final: 0.8238 (mp0) REVERT: B 677 GLU cc_start: 0.8403 (pt0) cc_final: 0.8126 (pt0) REVERT: B 680 LYS cc_start: 0.8987 (tttm) cc_final: 0.8785 (tttm) REVERT: B 711 ARG cc_start: 0.8580 (ttm110) cc_final: 0.8355 (ttm110) REVERT: B 712 GLN cc_start: 0.8123 (mm110) cc_final: 0.7922 (mm110) REVERT: B 715 LYS cc_start: 0.9015 (tptp) cc_final: 0.8755 (tppt) REVERT: B 833 LYS cc_start: 0.7575 (tptt) cc_final: 0.7336 (ttmm) REVERT: B 900 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8066 (pp) REVERT: B 1199 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7860 (mm-40) REVERT: C 82 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8140 (pt0) REVERT: C 227 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8531 (m-10) REVERT: C 310 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8435 (ptp90) REVERT: C 475 MET cc_start: 0.9418 (tpp) cc_final: 0.9025 (tpp) REVERT: C 595 LYS cc_start: 0.8770 (tppt) cc_final: 0.8364 (ttpm) REVERT: C 600 GLU cc_start: 0.8642 (mp0) cc_final: 0.8166 (mp0) REVERT: C 711 ARG cc_start: 0.8625 (ttm110) cc_final: 0.8401 (ttm110) REVERT: C 712 GLN cc_start: 0.7990 (mm110) cc_final: 0.7546 (mm110) REVERT: C 728 HIS cc_start: 0.7377 (m-70) cc_final: 0.6357 (t-90) REVERT: C 833 LYS cc_start: 0.7514 (tptt) cc_final: 0.7175 (ttmm) REVERT: C 859 GLU cc_start: 0.8686 (tt0) cc_final: 0.8461 (tt0) REVERT: C 900 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8093 (pp) REVERT: C 1053 GLU cc_start: 0.8231 (pm20) cc_final: 0.7933 (pm20) REVERT: C 1058 GLU cc_start: 0.8932 (tp30) cc_final: 0.8556 (tp30) REVERT: C 1199 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7697 (mm-40) REVERT: C 1242 VAL cc_start: 0.8256 (t) cc_final: 0.7913 (m) REVERT: D 6 PHE cc_start: 0.8080 (t80) cc_final: 0.7502 (t80) REVERT: D 9 LYS cc_start: 0.8275 (mmpt) cc_final: 0.7808 (mmpt) REVERT: D 82 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8242 (pt0) REVERT: D 227 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8448 (m-10) REVERT: D 310 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8417 (ptp90) REVERT: D 595 LYS cc_start: 0.8817 (tppt) cc_final: 0.8386 (tttp) REVERT: D 600 GLU cc_start: 0.8726 (mp0) cc_final: 0.8212 (mp0) REVERT: D 677 GLU cc_start: 0.8564 (pt0) cc_final: 0.8339 (pt0) REVERT: D 680 LYS cc_start: 0.8984 (tttm) cc_final: 0.8765 (tttm) REVERT: D 711 ARG cc_start: 0.8525 (ttm110) cc_final: 0.8288 (ttm110) REVERT: D 712 GLN cc_start: 0.8107 (mm110) cc_final: 0.7791 (mm110) REVERT: D 715 LYS cc_start: 0.9016 (tptp) cc_final: 0.8768 (tppt) REVERT: D 833 LYS cc_start: 0.7694 (tptt) cc_final: 0.7440 (ttmm) REVERT: D 969 ASP cc_start: 0.9030 (p0) cc_final: 0.8714 (p0) REVERT: D 1053 GLU cc_start: 0.8293 (pm20) cc_final: 0.7967 (pm20) outliers start: 182 outliers final: 96 residues processed: 829 average time/residue: 0.7020 time to fit residues: 706.4468 Evaluate side-chains 781 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 673 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1163 VAL Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1212 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 1000 ASP Chi-restraints excluded: chain C residue 1021 MET Chi-restraints excluded: chain C residue 1163 VAL Chi-restraints excluded: chain C residue 1174 VAL Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1219 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 310 ARG Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 650 VAL Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 832 SER Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 900 LEU Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1021 MET Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1174 VAL Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1220 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 365 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 447 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 228 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 chunk 92 optimal weight: 0.0870 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 ASN A1222 HIS B 754 ASN C 754 ASN D 754 ASN D1222 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.086677 restraints weight = 50633.941| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.69 r_work: 0.2844 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39008 Z= 0.149 Angle : 0.585 7.247 52976 Z= 0.307 Chirality : 0.044 0.179 5620 Planarity : 0.004 0.051 6856 Dihedral : 6.185 59.066 5190 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.33 % Allowed : 22.24 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.12), residues: 4696 helix: 1.47 (0.16), residues: 1148 sheet: -0.84 (0.14), residues: 1196 loop : -1.65 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 536 TYR 0.026 0.001 TYR D1170 PHE 0.011 0.001 PHE A 468 TRP 0.010 0.001 TRP B 769 HIS 0.006 0.001 HIS C 614 Details of bonding type rmsd covalent geometry : bond 0.00342 (39000) covalent geometry : angle 0.58464 (52976) hydrogen bonds : bond 0.04084 ( 1560) hydrogen bonds : angle 4.83020 ( 4368) metal coordination : bond 0.00176 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 716 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.9139 (m) REVERT: A 172 MET cc_start: 0.9153 (ttt) cc_final: 0.8908 (tmm) REVERT: A 227 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8529 (m-10) REVERT: A 595 LYS cc_start: 0.8766 (tppt) cc_final: 0.8351 (tttp) REVERT: A 600 GLU cc_start: 0.8624 (mp0) cc_final: 0.8204 (mp0) REVERT: A 623 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7451 (mt-10) REVERT: A 680 LYS cc_start: 0.8998 (tttm) cc_final: 0.8791 (tttm) REVERT: A 715 LYS cc_start: 0.8908 (tptp) cc_final: 0.8448 (tppt) REVERT: A 728 HIS cc_start: 0.7414 (m-70) cc_final: 0.6431 (t-90) REVERT: A 833 LYS cc_start: 0.7695 (tptt) cc_final: 0.7456 (ttmm) REVERT: A 1173 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.6902 (mtp-110) REVERT: A 1199 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7775 (mm-40) REVERT: A 1220 ILE cc_start: 0.8788 (mt) cc_final: 0.8527 (mp) REVERT: B 103 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.9088 (m) REVERT: B 172 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8866 (ttp) REVERT: B 200 LYS cc_start: 0.8583 (ptpp) cc_final: 0.7951 (ptpp) REVERT: B 227 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8509 (m-10) REVERT: B 310 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8359 (ptp90) REVERT: B 595 LYS cc_start: 0.8799 (tppt) cc_final: 0.8397 (ttpm) REVERT: B 600 GLU cc_start: 0.8615 (mp0) cc_final: 0.8279 (mp0) REVERT: B 677 GLU cc_start: 0.8399 (pt0) cc_final: 0.8106 (pt0) REVERT: B 700 LYS cc_start: 0.8696 (ttpp) cc_final: 0.8494 (ttpp) REVERT: B 712 GLN cc_start: 0.8114 (mm110) cc_final: 0.7656 (mm110) REVERT: B 715 LYS cc_start: 0.9001 (tptp) cc_final: 0.8778 (tppt) REVERT: B 728 HIS cc_start: 0.7365 (m-70) cc_final: 0.6407 (t-90) REVERT: B 833 LYS cc_start: 0.7559 (tptt) cc_final: 0.7325 (ttmm) REVERT: B 1053 GLU cc_start: 0.8291 (pm20) cc_final: 0.7907 (pm20) REVERT: B 1173 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7843 (mmp80) REVERT: B 1199 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7866 (mm-40) REVERT: C 82 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8219 (pt0) REVERT: C 103 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9126 (m) REVERT: C 310 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8387 (ptp90) REVERT: C 595 LYS cc_start: 0.8763 (tppt) cc_final: 0.8355 (ttpt) REVERT: C 600 GLU cc_start: 0.8614 (mp0) cc_final: 0.8133 (mp0) REVERT: C 644 MET cc_start: 0.8940 (tpt) cc_final: 0.8718 (tpt) REVERT: C 680 LYS cc_start: 0.8977 (tttm) cc_final: 0.8735 (tttm) REVERT: C 728 HIS cc_start: 0.7330 (m-70) cc_final: 0.6345 (t-90) REVERT: C 833 LYS cc_start: 0.7576 (tptt) cc_final: 0.7233 (ttmm) REVERT: C 889 ASP cc_start: 0.9204 (t70) cc_final: 0.8891 (t70) REVERT: C 1058 GLU cc_start: 0.8899 (tp30) cc_final: 0.8421 (tp30) REVERT: C 1199 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7716 (mm-40) REVERT: D 6 PHE cc_start: 0.8108 (t80) cc_final: 0.7522 (t80) REVERT: D 9 LYS cc_start: 0.8300 (mmpt) cc_final: 0.7624 (mmpt) REVERT: D 82 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8296 (pt0) REVERT: D 310 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8359 (ptp90) REVERT: D 595 LYS cc_start: 0.8826 (tppt) cc_final: 0.8381 (tttp) REVERT: D 600 GLU cc_start: 0.8676 (mp0) cc_final: 0.8278 (mp0) REVERT: D 677 GLU cc_start: 0.8573 (pt0) cc_final: 0.8336 (pt0) REVERT: D 680 LYS cc_start: 0.8949 (tttm) cc_final: 0.8720 (tttm) REVERT: D 715 LYS cc_start: 0.9004 (tptp) cc_final: 0.8760 (tppt) REVERT: D 728 HIS cc_start: 0.7446 (m-70) cc_final: 0.6545 (t-90) REVERT: D 833 LYS cc_start: 0.7654 (tptt) cc_final: 0.7418 (ttmm) REVERT: D 969 ASP cc_start: 0.9035 (p0) cc_final: 0.8718 (p0) REVERT: D 1053 GLU cc_start: 0.8242 (pm20) cc_final: 0.8033 (pm20) REVERT: D 1173 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7236 (mtp-110) outliers start: 177 outliers final: 101 residues processed: 838 average time/residue: 0.7018 time to fit residues: 714.7148 Evaluate side-chains 791 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 676 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1173 ARG Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1163 VAL Chi-restraints excluded: chain B residue 1173 ARG Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1212 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 1000 ASP Chi-restraints excluded: chain C residue 1163 VAL Chi-restraints excluded: chain C residue 1174 VAL Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1219 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 310 ARG Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 832 SER Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 900 LEU Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1173 ARG Chi-restraints excluded: chain D residue 1174 VAL Chi-restraints excluded: chain D residue 1212 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 50 optimal weight: 1.9990 chunk 218 optimal weight: 0.5980 chunk 276 optimal weight: 0.9990 chunk 263 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 422 optimal weight: 8.9990 chunk 366 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 317 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 ASN B 754 ASN C 754 ASN D 754 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.087092 restraints weight = 50658.231| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.68 r_work: 0.2845 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 39008 Z= 0.155 Angle : 0.586 8.415 52976 Z= 0.307 Chirality : 0.044 0.180 5620 Planarity : 0.004 0.052 6856 Dihedral : 6.068 59.348 5189 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.45 % Allowed : 22.56 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.12), residues: 4696 helix: 1.68 (0.16), residues: 1116 sheet: -0.83 (0.14), residues: 1208 loop : -1.55 (0.13), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 436 TYR 0.027 0.001 TYR D1170 PHE 0.011 0.001 PHE C 227 TRP 0.010 0.001 TRP B 769 HIS 0.006 0.001 HIS C 614 Details of bonding type rmsd covalent geometry : bond 0.00358 (39000) covalent geometry : angle 0.58551 (52976) hydrogen bonds : bond 0.04084 ( 1560) hydrogen bonds : angle 4.76893 ( 4368) metal coordination : bond 0.00193 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 715 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8509 (m-10) REVERT: A 310 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8400 (ptp90) REVERT: A 595 LYS cc_start: 0.8765 (tppt) cc_final: 0.8343 (tttp) REVERT: A 600 GLU cc_start: 0.8598 (mp0) cc_final: 0.8170 (mp0) REVERT: A 623 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7463 (mt-10) REVERT: A 711 ARG cc_start: 0.8709 (mtp85) cc_final: 0.8434 (mtp85) REVERT: A 715 LYS cc_start: 0.8882 (tptp) cc_final: 0.8449 (tppt) REVERT: A 728 HIS cc_start: 0.7369 (m-70) cc_final: 0.6407 (t-90) REVERT: A 833 LYS cc_start: 0.7756 (tptt) cc_final: 0.7477 (ttmm) REVERT: A 850 ASP cc_start: 0.8629 (t70) cc_final: 0.8377 (t0) REVERT: A 889 ASP cc_start: 0.9206 (t70) cc_final: 0.8866 (t70) REVERT: A 1058 GLU cc_start: 0.8873 (tp30) cc_final: 0.8001 (tp30) REVERT: A 1199 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7735 (mm-40) REVERT: B 200 LYS cc_start: 0.8622 (ptpp) cc_final: 0.7968 (ptpp) REVERT: B 226 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: B 310 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8368 (ptp90) REVERT: B 595 LYS cc_start: 0.8784 (tppt) cc_final: 0.8366 (ttpm) REVERT: B 600 GLU cc_start: 0.8592 (mp0) cc_final: 0.8288 (mp0) REVERT: B 677 GLU cc_start: 0.8383 (pt0) cc_final: 0.8088 (pt0) REVERT: B 680 LYS cc_start: 0.8953 (tttm) cc_final: 0.8650 (tttm) REVERT: B 700 LYS cc_start: 0.8660 (ttpp) cc_final: 0.8405 (ttpp) REVERT: B 712 GLN cc_start: 0.8131 (mm110) cc_final: 0.7547 (mm110) REVERT: B 715 LYS cc_start: 0.9000 (tptp) cc_final: 0.8769 (tppt) REVERT: B 728 HIS cc_start: 0.7357 (m-70) cc_final: 0.6382 (t-90) REVERT: B 833 LYS cc_start: 0.7621 (tptt) cc_final: 0.7358 (ttmm) REVERT: B 850 ASP cc_start: 0.8661 (t70) cc_final: 0.8443 (t0) REVERT: B 895 TYR cc_start: 0.9032 (t80) cc_final: 0.8824 (t80) REVERT: B 1053 GLU cc_start: 0.8270 (pm20) cc_final: 0.7945 (pm20) REVERT: B 1173 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7717 (mmp80) REVERT: B 1199 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7855 (mm-40) REVERT: C 82 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: C 226 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: C 227 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8635 (m-10) REVERT: C 310 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8403 (ptp90) REVERT: C 595 LYS cc_start: 0.8766 (tppt) cc_final: 0.8361 (ttpt) REVERT: C 600 GLU cc_start: 0.8568 (mp0) cc_final: 0.8134 (mp0) REVERT: C 644 MET cc_start: 0.8939 (tpt) cc_final: 0.8717 (tpt) REVERT: C 728 HIS cc_start: 0.7268 (m-70) cc_final: 0.6313 (t-90) REVERT: C 833 LYS cc_start: 0.7570 (tptt) cc_final: 0.7297 (ttmm) REVERT: C 889 ASP cc_start: 0.9205 (t70) cc_final: 0.9004 (t70) REVERT: C 895 TYR cc_start: 0.8996 (t80) cc_final: 0.8760 (t80) REVERT: C 969 ASP cc_start: 0.8913 (p0) cc_final: 0.8563 (p0) REVERT: C 1053 GLU cc_start: 0.8230 (pm20) cc_final: 0.7896 (pm20) REVERT: C 1058 GLU cc_start: 0.8875 (tp30) cc_final: 0.8421 (tp30) REVERT: C 1122 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6133 (mp) REVERT: C 1199 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7730 (mm-40) REVERT: D 6 PHE cc_start: 0.8105 (t80) cc_final: 0.7518 (t80) REVERT: D 9 LYS cc_start: 0.8268 (mmpt) cc_final: 0.7581 (mmpt) REVERT: D 82 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8368 (pt0) REVERT: D 200 LYS cc_start: 0.8530 (ptpp) cc_final: 0.7873 (ptpp) REVERT: D 226 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: D 227 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8458 (m-10) REVERT: D 310 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8350 (ptp90) REVERT: D 595 LYS cc_start: 0.8826 (tppt) cc_final: 0.8370 (tttp) REVERT: D 600 GLU cc_start: 0.8641 (mp0) cc_final: 0.8270 (mp0) REVERT: D 677 GLU cc_start: 0.8572 (pt0) cc_final: 0.8367 (pt0) REVERT: D 680 LYS cc_start: 0.8933 (tttm) cc_final: 0.8691 (tttm) REVERT: D 715 LYS cc_start: 0.8999 (tptp) cc_final: 0.8749 (tppt) REVERT: D 728 HIS cc_start: 0.7420 (m-70) cc_final: 0.6532 (t-90) REVERT: D 833 LYS cc_start: 0.7738 (tptt) cc_final: 0.7468 (ttmm) REVERT: D 850 ASP cc_start: 0.8662 (t70) cc_final: 0.8405 (t0) REVERT: D 895 TYR cc_start: 0.8993 (t80) cc_final: 0.8772 (t80) REVERT: D 969 ASP cc_start: 0.9014 (p0) cc_final: 0.8689 (p0) REVERT: D 1058 GLU cc_start: 0.8839 (tp30) cc_final: 0.8058 (tp30) REVERT: D 1173 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7277 (mtp-110) outliers start: 182 outliers final: 109 residues processed: 834 average time/residue: 0.7016 time to fit residues: 711.8752 Evaluate side-chains 805 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 681 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 892 GLU Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1163 VAL Chi-restraints excluded: chain B residue 1173 ARG Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1212 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 1000 ASP Chi-restraints excluded: chain C residue 1122 LEU Chi-restraints excluded: chain C residue 1163 VAL Chi-restraints excluded: chain C residue 1174 VAL Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1219 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 310 ARG Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 832 SER Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 900 LEU Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1173 ARG Chi-restraints excluded: chain D residue 1212 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 72 optimal weight: 2.9990 chunk 445 optimal weight: 3.9990 chunk 354 optimal weight: 0.0870 chunk 107 optimal weight: 4.9990 chunk 466 optimal weight: 6.9990 chunk 235 optimal weight: 3.9990 chunk 314 optimal weight: 0.9980 chunk 345 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 288 optimal weight: 3.9990 chunk 390 optimal weight: 0.9980 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 ASN B 754 ASN C 754 ASN D 754 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.087092 restraints weight = 50617.195| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.68 r_work: 0.2845 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 39008 Z= 0.161 Angle : 0.589 7.054 52976 Z= 0.308 Chirality : 0.044 0.190 5620 Planarity : 0.004 0.072 6856 Dihedral : 5.866 57.534 5180 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.13 % Allowed : 22.80 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.12), residues: 4696 helix: 1.48 (0.16), residues: 1148 sheet: -0.84 (0.14), residues: 1188 loop : -1.58 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 436 TYR 0.030 0.001 TYR D1170 PHE 0.011 0.001 PHE B 227 TRP 0.011 0.001 TRP D 769 HIS 0.006 0.001 HIS C 614 Details of bonding type rmsd covalent geometry : bond 0.00375 (39000) covalent geometry : angle 0.58872 (52976) hydrogen bonds : bond 0.04091 ( 1560) hydrogen bonds : angle 4.74580 ( 4368) metal coordination : bond 0.00200 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 708 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: A 227 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8538 (m-10) REVERT: A 310 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8396 (ptp90) REVERT: A 595 LYS cc_start: 0.8766 (tppt) cc_final: 0.8333 (tttp) REVERT: A 600 GLU cc_start: 0.8551 (mp0) cc_final: 0.8161 (mp0) REVERT: A 623 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7478 (mt-10) REVERT: A 711 ARG cc_start: 0.8738 (mtp85) cc_final: 0.8511 (mtp85) REVERT: A 715 LYS cc_start: 0.8886 (tptp) cc_final: 0.8448 (tppt) REVERT: A 728 HIS cc_start: 0.7371 (m-70) cc_final: 0.6389 (t-90) REVERT: A 850 ASP cc_start: 0.8691 (t70) cc_final: 0.8427 (t0) REVERT: A 889 ASP cc_start: 0.9194 (t70) cc_final: 0.8860 (t70) REVERT: A 999 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7923 (mm-30) REVERT: A 1058 GLU cc_start: 0.8872 (tp30) cc_final: 0.8012 (tp30) REVERT: A 1173 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7169 (mtp-110) REVERT: A 1199 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7763 (mm-40) REVERT: B 200 LYS cc_start: 0.8664 (ptpp) cc_final: 0.8027 (ptpp) REVERT: B 226 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: B 227 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8556 (m-10) REVERT: B 595 LYS cc_start: 0.8790 (tppt) cc_final: 0.8363 (ttpm) REVERT: B 600 GLU cc_start: 0.8578 (mp0) cc_final: 0.8204 (mp0) REVERT: B 677 GLU cc_start: 0.8374 (pt0) cc_final: 0.8047 (pt0) REVERT: B 712 GLN cc_start: 0.8137 (mm110) cc_final: 0.7785 (mm110) REVERT: B 715 LYS cc_start: 0.8992 (tptp) cc_final: 0.8766 (tppt) REVERT: B 728 HIS cc_start: 0.7341 (m-70) cc_final: 0.6375 (t-90) REVERT: B 833 LYS cc_start: 0.7612 (tptt) cc_final: 0.7359 (ttmm) REVERT: B 850 ASP cc_start: 0.8670 (t70) cc_final: 0.8468 (t0) REVERT: B 895 TYR cc_start: 0.9000 (t80) cc_final: 0.8748 (t80) REVERT: B 1030 ARG cc_start: 0.8562 (mtt-85) cc_final: 0.8275 (mmt90) REVERT: B 1053 GLU cc_start: 0.8284 (pm20) cc_final: 0.7960 (pm20) REVERT: C 82 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: C 226 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: C 227 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8602 (m-10) REVERT: C 595 LYS cc_start: 0.8766 (tppt) cc_final: 0.8346 (ttpm) REVERT: C 600 GLU cc_start: 0.8559 (mp0) cc_final: 0.8207 (mp0) REVERT: C 644 MET cc_start: 0.8939 (tpt) cc_final: 0.8735 (tpt) REVERT: C 680 LYS cc_start: 0.8967 (tttm) cc_final: 0.8433 (tptp) REVERT: C 728 HIS cc_start: 0.7262 (m-70) cc_final: 0.6322 (t-90) REVERT: C 833 LYS cc_start: 0.7569 (tptt) cc_final: 0.7302 (ttmm) REVERT: C 889 ASP cc_start: 0.9211 (t70) cc_final: 0.8879 (t70) REVERT: C 895 TYR cc_start: 0.9008 (t80) cc_final: 0.8794 (t80) REVERT: C 1053 GLU cc_start: 0.8185 (pm20) cc_final: 0.7860 (pm20) REVERT: C 1058 GLU cc_start: 0.8870 (tp30) cc_final: 0.8437 (tp30) REVERT: D 6 PHE cc_start: 0.8116 (t80) cc_final: 0.7534 (t80) REVERT: D 9 LYS cc_start: 0.8286 (mmpt) cc_final: 0.7721 (mmpt) REVERT: D 82 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8348 (pt0) REVERT: D 200 LYS cc_start: 0.8586 (ptpp) cc_final: 0.7929 (ptpp) REVERT: D 226 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: D 227 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8446 (m-10) REVERT: D 595 LYS cc_start: 0.8824 (tppt) cc_final: 0.8412 (ttpp) REVERT: D 600 GLU cc_start: 0.8644 (mp0) cc_final: 0.8238 (mp0) REVERT: D 677 GLU cc_start: 0.8588 (pt0) cc_final: 0.8288 (pt0) REVERT: D 728 HIS cc_start: 0.7425 (m-70) cc_final: 0.6512 (t-90) REVERT: D 833 LYS cc_start: 0.7738 (tptt) cc_final: 0.7476 (ttmm) REVERT: D 850 ASP cc_start: 0.8673 (t70) cc_final: 0.8424 (t0) REVERT: D 855 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: D 969 ASP cc_start: 0.9001 (p0) cc_final: 0.8694 (p0) REVERT: D 1058 GLU cc_start: 0.8826 (tp30) cc_final: 0.7954 (tp30) REVERT: D 1173 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.6992 (mtp-110) REVERT: D 1199 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7960 (mm-40) outliers start: 169 outliers final: 105 residues processed: 812 average time/residue: 0.7262 time to fit residues: 713.1066 Evaluate side-chains 810 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 691 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1173 ARG Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 892 GLU Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1163 VAL Chi-restraints excluded: chain B residue 1212 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 1000 ASP Chi-restraints excluded: chain C residue 1130 THR Chi-restraints excluded: chain C residue 1163 VAL Chi-restraints excluded: chain C residue 1174 VAL Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1219 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 832 SER Chi-restraints excluded: chain D residue 855 GLU Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 900 LEU Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1130 THR Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1173 ARG Chi-restraints excluded: chain D residue 1212 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 10 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 365 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 269 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 339 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 299 optimal weight: 0.9980 chunk 410 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 ASN B 754 ASN B1199 GLN C 754 ASN D 754 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.085846 restraints weight = 50711.121| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.73 r_work: 0.2815 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 39008 Z= 0.160 Angle : 0.592 9.482 52976 Z= 0.310 Chirality : 0.044 0.175 5620 Planarity : 0.004 0.064 6856 Dihedral : 5.785 55.163 5175 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.81 % Allowed : 23.75 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.12), residues: 4696 helix: 1.69 (0.16), residues: 1116 sheet: -0.86 (0.14), residues: 1208 loop : -1.52 (0.13), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 436 TYR 0.032 0.001 TYR A1170 PHE 0.010 0.001 PHE C 227 TRP 0.011 0.001 TRP B 769 HIS 0.006 0.001 HIS D 614 Details of bonding type rmsd covalent geometry : bond 0.00372 (39000) covalent geometry : angle 0.59210 (52976) hydrogen bonds : bond 0.04071 ( 1560) hydrogen bonds : angle 4.73176 ( 4368) metal coordination : bond 0.00194 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 725 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: A 227 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8391 (m-10) REVERT: A 310 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8295 (ptp90) REVERT: A 595 LYS cc_start: 0.8686 (tppt) cc_final: 0.8266 (tttp) REVERT: A 600 GLU cc_start: 0.8431 (mp0) cc_final: 0.7980 (mp0) REVERT: A 623 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7256 (mt-10) REVERT: A 680 LYS cc_start: 0.8916 (tttm) cc_final: 0.8271 (tptp) REVERT: A 711 ARG cc_start: 0.8671 (mtp85) cc_final: 0.8443 (mtp85) REVERT: A 715 LYS cc_start: 0.8842 (tptp) cc_final: 0.8429 (tppt) REVERT: A 728 HIS cc_start: 0.7107 (m-70) cc_final: 0.6161 (t-90) REVERT: A 850 ASP cc_start: 0.8556 (t70) cc_final: 0.8309 (t0) REVERT: A 855 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: A 889 ASP cc_start: 0.9070 (t70) cc_final: 0.8723 (t70) REVERT: A 999 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 1058 GLU cc_start: 0.8739 (tp30) cc_final: 0.7834 (tp30) REVERT: B 200 LYS cc_start: 0.8546 (ptpp) cc_final: 0.7885 (ptpp) REVERT: B 226 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6571 (mp0) REVERT: B 227 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8447 (m-10) REVERT: B 595 LYS cc_start: 0.8726 (tppt) cc_final: 0.8320 (ttpm) REVERT: B 600 GLU cc_start: 0.8456 (mp0) cc_final: 0.8058 (mp0) REVERT: B 677 GLU cc_start: 0.8052 (pt0) cc_final: 0.7745 (pt0) REVERT: B 680 LYS cc_start: 0.8934 (tttm) cc_final: 0.8386 (tptp) REVERT: B 700 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8378 (ttpp) REVERT: B 712 GLN cc_start: 0.8030 (mm110) cc_final: 0.7656 (mm110) REVERT: B 728 HIS cc_start: 0.7080 (m-70) cc_final: 0.6151 (t-90) REVERT: B 833 LYS cc_start: 0.7438 (tptt) cc_final: 0.7184 (ttmm) REVERT: B 1030 ARG cc_start: 0.8459 (mtt-85) cc_final: 0.8162 (mmt90) REVERT: B 1053 GLU cc_start: 0.8145 (pm20) cc_final: 0.7834 (pm20) REVERT: B 1199 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7756 (mm-40) REVERT: C 82 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: C 200 LYS cc_start: 0.8554 (ptpp) cc_final: 0.7869 (ptpp) REVERT: C 226 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.6558 (mp0) REVERT: C 227 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8460 (m-10) REVERT: C 310 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7387 (ptp90) REVERT: C 595 LYS cc_start: 0.8698 (tppt) cc_final: 0.8307 (ttpt) REVERT: C 600 GLU cc_start: 0.8440 (mp0) cc_final: 0.7976 (mp0) REVERT: C 644 MET cc_start: 0.8877 (tpt) cc_final: 0.8647 (tpt) REVERT: C 680 LYS cc_start: 0.8887 (tttm) cc_final: 0.8520 (tppp) REVERT: C 715 LYS cc_start: 0.8895 (tptp) cc_final: 0.8367 (tppt) REVERT: C 728 HIS cc_start: 0.7023 (m-70) cc_final: 0.6109 (t-90) REVERT: C 833 LYS cc_start: 0.7395 (tptt) cc_final: 0.7135 (ttmm) REVERT: C 889 ASP cc_start: 0.9065 (t70) cc_final: 0.8705 (t70) REVERT: C 969 ASP cc_start: 0.8867 (p0) cc_final: 0.8508 (p0) REVERT: C 1053 GLU cc_start: 0.8051 (pm20) cc_final: 0.7729 (pm20) REVERT: C 1058 GLU cc_start: 0.8764 (tp30) cc_final: 0.8375 (tp30) REVERT: C 1199 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7663 (mm-40) REVERT: D 6 PHE cc_start: 0.8062 (t80) cc_final: 0.7529 (t80) REVERT: D 9 LYS cc_start: 0.8284 (mmpt) cc_final: 0.7622 (mmpt) REVERT: D 82 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: D 200 LYS cc_start: 0.8481 (ptpp) cc_final: 0.7816 (ptpp) REVERT: D 226 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.6498 (mp0) REVERT: D 227 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8341 (m-10) REVERT: D 310 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7262 (ptp90) REVERT: D 595 LYS cc_start: 0.8727 (tppt) cc_final: 0.8325 (ttpp) REVERT: D 600 GLU cc_start: 0.8471 (mp0) cc_final: 0.8038 (mp0) REVERT: D 680 LYS cc_start: 0.9016 (ttpp) cc_final: 0.8537 (tttm) REVERT: D 728 HIS cc_start: 0.7190 (m-70) cc_final: 0.6312 (t-90) REVERT: D 969 ASP cc_start: 0.8939 (p0) cc_final: 0.8616 (p0) REVERT: D 1058 GLU cc_start: 0.8699 (tp30) cc_final: 0.7800 (tp30) REVERT: D 1173 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7050 (mtp-110) REVERT: D 1199 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7930 (mm-40) outliers start: 156 outliers final: 108 residues processed: 820 average time/residue: 0.7114 time to fit residues: 704.8289 Evaluate side-chains 813 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 690 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1163 VAL Chi-restraints excluded: chain B residue 1212 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 1000 ASP Chi-restraints excluded: chain C residue 1130 THR Chi-restraints excluded: chain C residue 1174 VAL Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1219 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 310 ARG Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 832 SER Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 900 LEU Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1130 THR Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1173 ARG Chi-restraints excluded: chain D residue 1212 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 147 optimal weight: 1.9990 chunk 277 optimal weight: 0.9990 chunk 410 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 448 optimal weight: 3.9990 chunk 389 optimal weight: 2.9990 chunk 304 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 402 optimal weight: 3.9990 chunk 308 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 ASN A1199 GLN B 754 ASN C 754 ASN D 754 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.086385 restraints weight = 50481.900| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.73 r_work: 0.2827 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 39008 Z= 0.155 Angle : 0.602 8.323 52976 Z= 0.316 Chirality : 0.044 0.190 5620 Planarity : 0.005 0.081 6856 Dihedral : 5.754 57.399 5174 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.86 % Allowed : 24.29 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.12), residues: 4696 helix: 1.70 (0.16), residues: 1116 sheet: -0.81 (0.14), residues: 1200 loop : -1.53 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1030 TYR 0.036 0.001 TYR D1170 PHE 0.010 0.001 PHE C 227 TRP 0.011 0.001 TRP B 769 HIS 0.006 0.001 HIS D 614 Details of bonding type rmsd covalent geometry : bond 0.00361 (39000) covalent geometry : angle 0.60210 (52976) hydrogen bonds : bond 0.04013 ( 1560) hydrogen bonds : angle 4.73068 ( 4368) metal coordination : bond 0.00175 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 719 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.9333 (OUTLIER) cc_final: 0.9122 (m) REVERT: A 226 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.6612 (mp0) REVERT: A 227 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8385 (m-10) REVERT: A 310 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8243 (ptp90) REVERT: A 595 LYS cc_start: 0.8671 (tppt) cc_final: 0.8263 (tttp) REVERT: A 600 GLU cc_start: 0.8461 (mp0) cc_final: 0.8001 (mp0) REVERT: A 623 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7276 (mt-10) REVERT: A 680 LYS cc_start: 0.8932 (tttm) cc_final: 0.8476 (tptp) REVERT: A 715 LYS cc_start: 0.8837 (tptp) cc_final: 0.8441 (tppt) REVERT: A 728 HIS cc_start: 0.7098 (m-70) cc_final: 0.6161 (t-90) REVERT: A 850 ASP cc_start: 0.8527 (t70) cc_final: 0.8265 (OUTLIER) REVERT: A 855 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: A 889 ASP cc_start: 0.9062 (t70) cc_final: 0.8709 (t70) REVERT: A 999 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7787 (mm-30) REVERT: A 1058 GLU cc_start: 0.8732 (tp30) cc_final: 0.7813 (tp30) REVERT: A 1173 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7430 (mmt-90) REVERT: A 1199 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7580 (mm-40) REVERT: B 200 LYS cc_start: 0.8546 (ptpp) cc_final: 0.7899 (ptpp) REVERT: B 226 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: B 227 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8400 (m-10) REVERT: B 595 LYS cc_start: 0.8734 (tppt) cc_final: 0.8311 (ttpm) REVERT: B 600 GLU cc_start: 0.8456 (mp0) cc_final: 0.8100 (mp0) REVERT: B 644 MET cc_start: 0.8913 (tpt) cc_final: 0.8697 (tpt) REVERT: B 677 GLU cc_start: 0.8026 (pt0) cc_final: 0.7712 (pt0) REVERT: B 680 LYS cc_start: 0.8853 (tttm) cc_final: 0.8328 (tptp) REVERT: B 700 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8354 (ttpp) REVERT: B 712 GLN cc_start: 0.8014 (mm110) cc_final: 0.7625 (mm110) REVERT: B 728 HIS cc_start: 0.7064 (m-70) cc_final: 0.6151 (t-90) REVERT: B 833 LYS cc_start: 0.7436 (tptt) cc_final: 0.7235 (ttmm) REVERT: B 1053 GLU cc_start: 0.8156 (pm20) cc_final: 0.7828 (pm20) REVERT: B 1199 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7741 (mm-40) REVERT: C 82 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: C 200 LYS cc_start: 0.8573 (ptpp) cc_final: 0.7900 (ptpp) REVERT: C 226 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: C 227 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8452 (m-10) REVERT: C 310 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7504 (ptp90) REVERT: C 595 LYS cc_start: 0.8693 (tppt) cc_final: 0.8304 (ttpt) REVERT: C 600 GLU cc_start: 0.8434 (mp0) cc_final: 0.7975 (mp0) REVERT: C 644 MET cc_start: 0.8876 (tpt) cc_final: 0.8646 (tpt) REVERT: C 680 LYS cc_start: 0.8889 (tttm) cc_final: 0.8638 (tttm) REVERT: C 711 ARG cc_start: 0.8777 (mtp85) cc_final: 0.8478 (mtp85) REVERT: C 715 LYS cc_start: 0.8870 (tptp) cc_final: 0.8411 (tppt) REVERT: C 728 HIS cc_start: 0.7011 (m-70) cc_final: 0.6109 (t-90) REVERT: C 833 LYS cc_start: 0.7391 (tptt) cc_final: 0.7128 (ttmm) REVERT: C 889 ASP cc_start: 0.9063 (t70) cc_final: 0.8698 (t70) REVERT: C 969 ASP cc_start: 0.8849 (p0) cc_final: 0.8519 (p0) REVERT: C 1053 GLU cc_start: 0.8062 (pm20) cc_final: 0.7701 (pm20) REVERT: C 1058 GLU cc_start: 0.8748 (tp30) cc_final: 0.8386 (tp30) REVERT: C 1199 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7622 (mm-40) REVERT: C 1238 TRP cc_start: 0.7725 (p90) cc_final: 0.7370 (p90) REVERT: D 6 PHE cc_start: 0.8057 (t80) cc_final: 0.7526 (t80) REVERT: D 9 LYS cc_start: 0.8266 (mmpt) cc_final: 0.7634 (mmpt) REVERT: D 82 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: D 200 LYS cc_start: 0.8491 (ptpp) cc_final: 0.7806 (ptpp) REVERT: D 226 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.6481 (mp0) REVERT: D 227 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8351 (m-10) REVERT: D 595 LYS cc_start: 0.8730 (tppt) cc_final: 0.8325 (ttpp) REVERT: D 600 GLU cc_start: 0.8481 (mp0) cc_final: 0.8086 (mp0) REVERT: D 644 MET cc_start: 0.8960 (tpt) cc_final: 0.8715 (tpt) REVERT: D 680 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8499 (tttm) REVERT: D 700 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8151 (ttpt) REVERT: D 728 HIS cc_start: 0.7168 (m-70) cc_final: 0.6304 (t-90) REVERT: D 969 ASP cc_start: 0.8919 (p0) cc_final: 0.8621 (p0) REVERT: D 1058 GLU cc_start: 0.8701 (tp30) cc_final: 0.8104 (tp30) REVERT: D 1173 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7005 (mtp-110) REVERT: D 1199 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7927 (mm-40) outliers start: 158 outliers final: 102 residues processed: 812 average time/residue: 0.7132 time to fit residues: 702.0302 Evaluate side-chains 814 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 697 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1173 ARG Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1130 THR Chi-restraints excluded: chain B residue 1212 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 1000 ASP Chi-restraints excluded: chain C residue 1130 THR Chi-restraints excluded: chain C residue 1163 VAL Chi-restraints excluded: chain C residue 1174 VAL Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1219 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 832 SER Chi-restraints excluded: chain D residue 900 LEU Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1130 THR Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1173 ARG Chi-restraints excluded: chain D residue 1212 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 399 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 402 optimal weight: 0.0040 chunk 216 optimal weight: 0.7980 chunk 246 optimal weight: 0.8980 chunk 391 optimal weight: 0.9980 chunk 388 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS A 754 ASN B 754 ASN C 754 ASN D 754 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.108428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.088359 restraints weight = 50538.481| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.73 r_work: 0.2856 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39008 Z= 0.130 Angle : 0.588 7.808 52976 Z= 0.308 Chirality : 0.043 0.176 5620 Planarity : 0.004 0.070 6856 Dihedral : 5.506 59.383 5167 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.13 % Allowed : 25.34 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.12), residues: 4696 helix: 1.77 (0.16), residues: 1116 sheet: -0.82 (0.14), residues: 1200 loop : -1.53 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 436 TYR 0.033 0.001 TYR A1170 PHE 0.009 0.001 PHE C 227 TRP 0.010 0.001 TRP B 836 HIS 0.011 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00299 (39000) covalent geometry : angle 0.58829 (52976) hydrogen bonds : bond 0.03743 ( 1560) hydrogen bonds : angle 4.65904 ( 4368) metal coordination : bond 0.00127 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 748 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8564 (mp) cc_final: 0.8297 (mt) REVERT: A 103 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9154 (m) REVERT: A 226 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: A 227 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8349 (m-10) REVERT: A 310 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8211 (ptp90) REVERT: A 595 LYS cc_start: 0.8676 (tppt) cc_final: 0.8282 (tttp) REVERT: A 600 GLU cc_start: 0.8486 (mp0) cc_final: 0.8034 (mp0) REVERT: A 623 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7250 (mt-10) REVERT: A 680 LYS cc_start: 0.8931 (tttm) cc_final: 0.8483 (tptp) REVERT: A 711 ARG cc_start: 0.8685 (mtp85) cc_final: 0.8315 (mtp85) REVERT: A 715 LYS cc_start: 0.8782 (tptp) cc_final: 0.8353 (tppt) REVERT: A 721 GLU cc_start: 0.7938 (tt0) cc_final: 0.7600 (tt0) REVERT: A 728 HIS cc_start: 0.7055 (m-70) cc_final: 0.6162 (t-90) REVERT: A 850 ASP cc_start: 0.8558 (t70) cc_final: 0.8322 (OUTLIER) REVERT: A 855 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: A 889 ASP cc_start: 0.9037 (t70) cc_final: 0.8646 (t70) REVERT: A 999 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7763 (mm-30) REVERT: A 1058 GLU cc_start: 0.8688 (tp30) cc_final: 0.7757 (tp30) REVERT: A 1170 TYR cc_start: 0.8686 (t80) cc_final: 0.8482 (t80) REVERT: A 1173 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7435 (mmt-90) REVERT: A 1199 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7614 (mm-40) REVERT: A 1242 VAL cc_start: 0.8024 (t) cc_final: 0.7687 (m) REVERT: B 67 LEU cc_start: 0.8493 (mp) cc_final: 0.8220 (mt) REVERT: B 82 GLU cc_start: 0.8333 (pt0) cc_final: 0.7734 (tm-30) REVERT: B 127 ASP cc_start: 0.8703 (t0) cc_final: 0.8347 (t0) REVERT: B 200 LYS cc_start: 0.8592 (ptpp) cc_final: 0.7954 (ptpp) REVERT: B 226 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: B 227 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8375 (m-10) REVERT: B 310 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7331 (ptp90) REVERT: B 595 LYS cc_start: 0.8729 (tppt) cc_final: 0.8319 (ttpt) REVERT: B 600 GLU cc_start: 0.8528 (mp0) cc_final: 0.8144 (mp0) REVERT: B 677 GLU cc_start: 0.7987 (pt0) cc_final: 0.7691 (pt0) REVERT: B 680 LYS cc_start: 0.8881 (tttm) cc_final: 0.8370 (tptp) REVERT: B 700 LYS cc_start: 0.8642 (ttpp) cc_final: 0.8341 (ttpp) REVERT: B 712 GLN cc_start: 0.7982 (mm110) cc_final: 0.7580 (mm110) REVERT: B 721 GLU cc_start: 0.7903 (tt0) cc_final: 0.7688 (tt0) REVERT: B 728 HIS cc_start: 0.7144 (m-70) cc_final: 0.6162 (t-90) REVERT: B 1053 GLU cc_start: 0.8112 (pm20) cc_final: 0.7686 (pm20) REVERT: B 1199 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7765 (mm-40) REVERT: C 82 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: C 200 LYS cc_start: 0.8569 (ptpp) cc_final: 0.7902 (ptpp) REVERT: C 226 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.6556 (mp0) REVERT: C 227 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8418 (m-10) REVERT: C 282 GLU cc_start: 0.8501 (tp30) cc_final: 0.8184 (tp30) REVERT: C 595 LYS cc_start: 0.8689 (tppt) cc_final: 0.8304 (ttpt) REVERT: C 600 GLU cc_start: 0.8429 (mp0) cc_final: 0.8001 (mp0) REVERT: C 644 MET cc_start: 0.8855 (tpt) cc_final: 0.8627 (tpt) REVERT: C 680 LYS cc_start: 0.8846 (tttm) cc_final: 0.8603 (tttm) REVERT: C 711 ARG cc_start: 0.8707 (mtp85) cc_final: 0.8457 (mtp85) REVERT: C 715 LYS cc_start: 0.8857 (tptp) cc_final: 0.8420 (tppt) REVERT: C 728 HIS cc_start: 0.7092 (m-70) cc_final: 0.6135 (t-90) REVERT: C 833 LYS cc_start: 0.7389 (tptt) cc_final: 0.7120 (ttmm) REVERT: C 889 ASP cc_start: 0.9038 (t70) cc_final: 0.8684 (t70) REVERT: C 969 ASP cc_start: 0.8838 (p0) cc_final: 0.8500 (p0) REVERT: C 1053 GLU cc_start: 0.8038 (pm20) cc_final: 0.7419 (pm20) REVERT: C 1058 GLU cc_start: 0.8683 (tp30) cc_final: 0.8366 (tp30) REVERT: C 1199 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7635 (mm-40) REVERT: C 1238 TRP cc_start: 0.7703 (p90) cc_final: 0.7303 (p90) REVERT: D 6 PHE cc_start: 0.8050 (t80) cc_final: 0.7506 (t80) REVERT: D 9 LYS cc_start: 0.8354 (mmpt) cc_final: 0.7711 (mmpt) REVERT: D 67 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8400 (mp) REVERT: D 200 LYS cc_start: 0.8517 (ptpp) cc_final: 0.7876 (ptpp) REVERT: D 226 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: D 227 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8310 (m-10) REVERT: D 282 GLU cc_start: 0.8439 (tp30) cc_final: 0.8144 (tp30) REVERT: D 310 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7306 (ptp90) REVERT: D 595 LYS cc_start: 0.8743 (tppt) cc_final: 0.8327 (ttpp) REVERT: D 600 GLU cc_start: 0.8471 (mp0) cc_final: 0.8116 (mp0) REVERT: D 680 LYS cc_start: 0.8981 (ttpp) cc_final: 0.8526 (tttm) REVERT: D 700 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8343 (ttpp) REVERT: D 728 HIS cc_start: 0.7131 (m-70) cc_final: 0.6321 (t-90) REVERT: D 969 ASP cc_start: 0.8943 (p0) cc_final: 0.8637 (p0) REVERT: D 1058 GLU cc_start: 0.8664 (tp30) cc_final: 0.8249 (tp30) REVERT: D 1122 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6455 (mp) REVERT: D 1199 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7903 (mm-40) REVERT: D 1240 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7865 (t70) outliers start: 128 outliers final: 85 residues processed: 822 average time/residue: 0.7062 time to fit residues: 703.7236 Evaluate side-chains 808 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 706 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 840 MET Chi-restraints excluded: chain A residue 855 GLU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1173 ARG Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1163 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 1000 ASP Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1163 VAL Chi-restraints excluded: chain C residue 1174 VAL Chi-restraints excluded: chain C residue 1219 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 310 ARG Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 832 SER Chi-restraints excluded: chain D residue 900 LEU Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1122 LEU Chi-restraints excluded: chain D residue 1130 THR Chi-restraints excluded: chain D residue 1240 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 299 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 67 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 109 optimal weight: 0.0070 chunk 135 optimal weight: 3.9990 chunk 399 optimal weight: 0.5980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS A 754 ASN B 754 ASN C 754 ASN D 754 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.088597 restraints weight = 50224.442| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.72 r_work: 0.2859 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39008 Z= 0.130 Angle : 0.596 10.131 52976 Z= 0.311 Chirality : 0.043 0.176 5620 Planarity : 0.005 0.077 6856 Dihedral : 5.306 58.326 5162 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.61 % Allowed : 26.34 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.12), residues: 4696 helix: 1.77 (0.16), residues: 1116 sheet: -0.82 (0.14), residues: 1200 loop : -1.53 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 436 TYR 0.032 0.001 TYR A1170 PHE 0.019 0.001 PHE C 406 TRP 0.011 0.001 TRP A 836 HIS 0.023 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00302 (39000) covalent geometry : angle 0.59598 (52976) hydrogen bonds : bond 0.03726 ( 1560) hydrogen bonds : angle 4.63989 ( 4368) metal coordination : bond 0.00137 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 726 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: A 227 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8342 (m-10) REVERT: A 310 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8209 (ptp90) REVERT: A 595 LYS cc_start: 0.8669 (tppt) cc_final: 0.8278 (tttp) REVERT: A 600 GLU cc_start: 0.8483 (mp0) cc_final: 0.8037 (mp0) REVERT: A 623 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7247 (mt-10) REVERT: A 680 LYS cc_start: 0.8921 (tttm) cc_final: 0.8461 (tptp) REVERT: A 711 ARG cc_start: 0.8680 (mtp85) cc_final: 0.8292 (mtp85) REVERT: A 715 LYS cc_start: 0.8851 (tptp) cc_final: 0.8380 (tppt) REVERT: A 721 GLU cc_start: 0.7926 (tt0) cc_final: 0.7591 (tt0) REVERT: A 728 HIS cc_start: 0.7137 (m-70) cc_final: 0.6145 (t-90) REVERT: A 850 ASP cc_start: 0.8536 (t70) cc_final: 0.8312 (OUTLIER) REVERT: A 855 GLU cc_start: 0.8110 (tt0) cc_final: 0.7867 (tt0) REVERT: A 889 ASP cc_start: 0.9038 (t70) cc_final: 0.8641 (t70) REVERT: A 999 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7757 (mm-30) REVERT: A 1058 GLU cc_start: 0.8639 (tp30) cc_final: 0.8344 (tp30) REVERT: A 1173 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7467 (mmt-90) REVERT: A 1199 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7606 (mm-40) REVERT: A 1242 VAL cc_start: 0.7949 (t) cc_final: 0.7609 (m) REVERT: B 82 GLU cc_start: 0.8304 (pt0) cc_final: 0.7674 (tm-30) REVERT: B 127 ASP cc_start: 0.8711 (t0) cc_final: 0.8336 (t0) REVERT: B 200 LYS cc_start: 0.8572 (ptpp) cc_final: 0.7887 (ptpp) REVERT: B 226 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: B 227 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8351 (m-10) REVERT: B 595 LYS cc_start: 0.8729 (tppt) cc_final: 0.8319 (ttpt) REVERT: B 600 GLU cc_start: 0.8526 (mp0) cc_final: 0.8158 (mp0) REVERT: B 677 GLU cc_start: 0.8002 (pt0) cc_final: 0.7674 (pt0) REVERT: B 680 LYS cc_start: 0.8854 (tttm) cc_final: 0.8312 (tptp) REVERT: B 700 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8333 (ttpp) REVERT: B 712 GLN cc_start: 0.7991 (mm110) cc_final: 0.7495 (mm110) REVERT: B 721 GLU cc_start: 0.7864 (tt0) cc_final: 0.7652 (tt0) REVERT: B 728 HIS cc_start: 0.7126 (m-70) cc_final: 0.6151 (t-90) REVERT: B 731 LYS cc_start: 0.8650 (ptpp) cc_final: 0.8257 (ptmm) REVERT: B 1053 GLU cc_start: 0.8116 (pm20) cc_final: 0.7685 (pm20) REVERT: B 1199 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7763 (mm-40) REVERT: C 82 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: C 200 LYS cc_start: 0.8563 (ptpp) cc_final: 0.7923 (ptpp) REVERT: C 226 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.6553 (mp0) REVERT: C 227 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8415 (m-10) REVERT: C 595 LYS cc_start: 0.8651 (tppt) cc_final: 0.8258 (ttpt) REVERT: C 600 GLU cc_start: 0.8488 (mp0) cc_final: 0.7962 (mp0) REVERT: C 644 MET cc_start: 0.8856 (tpt) cc_final: 0.8655 (tpt) REVERT: C 680 LYS cc_start: 0.8847 (tttm) cc_final: 0.8607 (tttm) REVERT: C 711 ARG cc_start: 0.8686 (mtp85) cc_final: 0.8438 (mtp85) REVERT: C 715 LYS cc_start: 0.8861 (tptp) cc_final: 0.8425 (tppt) REVERT: C 728 HIS cc_start: 0.7078 (m-70) cc_final: 0.6131 (t-90) REVERT: C 833 LYS cc_start: 0.7390 (tptt) cc_final: 0.7121 (ttmm) REVERT: C 889 ASP cc_start: 0.9044 (t70) cc_final: 0.8677 (t70) REVERT: C 969 ASP cc_start: 0.8817 (p0) cc_final: 0.8496 (p0) REVERT: C 999 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7698 (mm-30) REVERT: C 1053 GLU cc_start: 0.8041 (pm20) cc_final: 0.7420 (pm20) REVERT: C 1058 GLU cc_start: 0.8669 (tp30) cc_final: 0.8344 (tp30) REVERT: C 1199 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7626 (mm-40) REVERT: C 1238 TRP cc_start: 0.7670 (p90) cc_final: 0.7234 (p90) REVERT: D 6 PHE cc_start: 0.8051 (t80) cc_final: 0.7510 (t80) REVERT: D 9 LYS cc_start: 0.8369 (mmpt) cc_final: 0.7677 (mmpt) REVERT: D 200 LYS cc_start: 0.8503 (ptpp) cc_final: 0.7885 (ptpp) REVERT: D 226 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: D 227 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8359 (m-10) REVERT: D 310 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7289 (ptp90) REVERT: D 595 LYS cc_start: 0.8746 (tppt) cc_final: 0.8326 (ttpp) REVERT: D 600 GLU cc_start: 0.8461 (mp0) cc_final: 0.8088 (mp0) REVERT: D 680 LYS cc_start: 0.8980 (ttpp) cc_final: 0.8538 (tttm) REVERT: D 700 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8343 (ttpp) REVERT: D 728 HIS cc_start: 0.7113 (m-70) cc_final: 0.6312 (t-90) REVERT: D 969 ASP cc_start: 0.9001 (p0) cc_final: 0.8689 (p0) REVERT: D 1058 GLU cc_start: 0.8652 (tp30) cc_final: 0.8227 (tp30) REVERT: D 1199 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7947 (mm-40) outliers start: 107 outliers final: 82 residues processed: 787 average time/residue: 0.7097 time to fit residues: 683.2902 Evaluate side-chains 804 residues out of total 4100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 711 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1173 ARG Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1163 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 559 THR Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 1000 ASP Chi-restraints excluded: chain C residue 1163 VAL Chi-restraints excluded: chain C residue 1174 VAL Chi-restraints excluded: chain C residue 1219 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 310 ARG Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 641 GLU Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 832 SER Chi-restraints excluded: chain D residue 900 LEU Chi-restraints excluded: chain D residue 1130 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 376 optimal weight: 0.9990 chunk 427 optimal weight: 5.9990 chunk 468 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 221 optimal weight: 0.8980 chunk 211 optimal weight: 6.9990 chunk 120 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 469 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS A 754 ASN B 754 ASN C 754 ASN D 754 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.088825 restraints weight = 50405.293| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.73 r_work: 0.2868 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39008 Z= 0.131 Angle : 0.596 12.263 52976 Z= 0.311 Chirality : 0.043 0.204 5620 Planarity : 0.005 0.078 6856 Dihedral : 5.222 52.230 5160 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.71 % Allowed : 26.34 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.12), residues: 4696 helix: 1.78 (0.16), residues: 1116 sheet: -0.80 (0.14), residues: 1200 loop : -1.53 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 436 TYR 0.040 0.001 TYR D1170 PHE 0.018 0.001 PHE C 406 TRP 0.012 0.001 TRP A1238 HIS 0.024 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00305 (39000) covalent geometry : angle 0.59570 (52976) hydrogen bonds : bond 0.03717 ( 1560) hydrogen bonds : angle 4.62356 ( 4368) metal coordination : bond 0.00138 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16454.96 seconds wall clock time: 280 minutes 2.85 seconds (16802.85 seconds total)