Starting phenix.real_space_refine on Tue Aug 26 03:10:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vt0_43514/08_2025/8vt0_43514.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vt0_43514/08_2025/8vt0_43514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vt0_43514/08_2025/8vt0_43514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vt0_43514/08_2025/8vt0_43514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vt0_43514/08_2025/8vt0_43514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vt0_43514/08_2025/8vt0_43514.map" } resolution = 3.58 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= 0.005 sd= 0.052 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 Mg 4 5.21 5 S 156 5.16 5 C 20760 2.51 5 N 5808 2.21 5 O 6100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32828 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 11, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 948} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 10.37, per 1000 atoms: 0.32 Number of scatterers: 32828 At special positions: 0 Unit cell: (159.84, 110.88, 200.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 Mg 4 11.99 O 6100 8.00 N 5808 7.00 C 20760 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: 2.78 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7608 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 52 sheets defined 12.7% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 removed outlier: 4.023A pdb=" N LEU A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.891A pdb=" N THR A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.817A pdb=" N TRP A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 74' Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.588A pdb=" N LEU A 134 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 removed outlier: 3.757A pdb=" N GLU A 198 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.839A pdb=" N VAL A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN A 374 " --> pdb=" O GLN A 370 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 376 " --> pdb=" O MET A 372 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.521A pdb=" N ASP A 428 " --> pdb=" O ASN A 424 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 429' Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 471 through 479 removed outlier: 3.684A pdb=" N VAL A 478 " --> pdb=" O TRP A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 551 through 559 removed outlier: 3.886A pdb=" N ALA A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG A 557 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 621 removed outlier: 4.087A pdb=" N ALA A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 793 removed outlier: 3.736A pdb=" N ASP A 792 " --> pdb=" O LEU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 814 Processing helix chain 'A' and resid 923 through 925 No H-bonds generated for 'chain 'A' and resid 923 through 925' Processing helix chain 'A' and resid 964 through 970 removed outlier: 3.748A pdb=" N MET A 968 " --> pdb=" O GLN A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 removed outlier: 3.635A pdb=" N PHE A1007 " --> pdb=" O SER A1004 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A1008 " --> pdb=" O ALA A1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1004 through 1008' Processing helix chain 'B' and resid 6 through 12 removed outlier: 4.021A pdb=" N LEU B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.890A pdb=" N THR B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.817A pdb=" N TRP B 73 " --> pdb=" O PRO B 70 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 74' Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.587A pdb=" N LEU B 134 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 removed outlier: 3.756A pdb=" N GLU B 198 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 381 removed outlier: 3.840A pdb=" N VAL B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN B 374 " --> pdb=" O GLN B 370 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 376 " --> pdb=" O MET B 372 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 424 through 429 removed outlier: 3.522A pdb=" N ASP B 428 " --> pdb=" O ASN B 424 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 424 through 429' Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 471 through 479 removed outlier: 3.683A pdb=" N VAL B 478 " --> pdb=" O TRP B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing helix chain 'B' and resid 551 through 559 removed outlier: 3.885A pdb=" N ALA B 555 " --> pdb=" O LYS B 551 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ARG B 557 " --> pdb=" O TRP B 553 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 621 removed outlier: 4.087A pdb=" N ALA B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 793 removed outlier: 3.736A pdb=" N ASP B 792 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 814 Processing helix chain 'B' and resid 923 through 925 No H-bonds generated for 'chain 'B' and resid 923 through 925' Processing helix chain 'B' and resid 964 through 970 removed outlier: 3.748A pdb=" N MET B 968 " --> pdb=" O GLN B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1008 removed outlier: 3.635A pdb=" N PHE B1007 " --> pdb=" O SER B1004 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B1008 " --> pdb=" O ALA B1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1004 through 1008' Processing helix chain 'C' and resid 6 through 12 removed outlier: 4.022A pdb=" N LEU C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN C 12 " --> pdb=" O ALA C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.891A pdb=" N THR C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.817A pdb=" N TRP C 73 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 74' Processing helix chain 'C' and resid 131 through 135 removed outlier: 3.588A pdb=" N LEU C 134 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 removed outlier: 3.757A pdb=" N GLU C 198 " --> pdb=" O SER C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 381 removed outlier: 3.840A pdb=" N VAL C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN C 374 " --> pdb=" O GLN C 370 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 376 " --> pdb=" O MET C 372 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 424 through 429 removed outlier: 3.521A pdb=" N ASP C 428 " --> pdb=" O ASN C 424 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 424 through 429' Processing helix chain 'C' and resid 432 through 437 Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 466 through 471 Processing helix chain 'C' and resid 471 through 479 removed outlier: 3.683A pdb=" N VAL C 478 " --> pdb=" O TRP C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 550 No H-bonds generated for 'chain 'C' and resid 548 through 550' Processing helix chain 'C' and resid 551 through 559 removed outlier: 3.886A pdb=" N ALA C 555 " --> pdb=" O LYS C 551 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG C 557 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 621 removed outlier: 4.088A pdb=" N ALA C 620 " --> pdb=" O ALA C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 793 removed outlier: 3.736A pdb=" N ASP C 792 " --> pdb=" O LEU C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 814 Processing helix chain 'C' and resid 923 through 925 No H-bonds generated for 'chain 'C' and resid 923 through 925' Processing helix chain 'C' and resid 964 through 970 removed outlier: 3.748A pdb=" N MET C 968 " --> pdb=" O GLN C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1008 removed outlier: 3.635A pdb=" N PHE C1007 " --> pdb=" O SER C1004 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C1008 " --> pdb=" O ALA C1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1004 through 1008' Processing helix chain 'D' and resid 6 through 12 removed outlier: 4.022A pdb=" N LEU D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN D 12 " --> pdb=" O ALA D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.891A pdb=" N THR D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.816A pdb=" N TRP D 73 " --> pdb=" O PRO D 70 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 74 " --> pdb=" O GLU D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 74' Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.587A pdb=" N LEU D 134 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 198 removed outlier: 3.756A pdb=" N GLU D 198 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 381 removed outlier: 3.839A pdb=" N VAL D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN D 374 " --> pdb=" O GLN D 370 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D 376 " --> pdb=" O MET D 372 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 424 through 429 removed outlier: 3.521A pdb=" N ASP D 428 " --> pdb=" O ASN D 424 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 424 through 429' Processing helix chain 'D' and resid 432 through 437 Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'D' and resid 466 through 471 Processing helix chain 'D' and resid 471 through 479 removed outlier: 3.683A pdb=" N VAL D 478 " --> pdb=" O TRP D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 550 No H-bonds generated for 'chain 'D' and resid 548 through 550' Processing helix chain 'D' and resid 551 through 559 removed outlier: 3.886A pdb=" N ALA D 555 " --> pdb=" O LYS D 551 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG D 557 " --> pdb=" O TRP D 553 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D 559 " --> pdb=" O ALA D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 621 removed outlier: 4.087A pdb=" N ALA D 620 " --> pdb=" O ALA D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 793 removed outlier: 3.735A pdb=" N ASP D 792 " --> pdb=" O LEU D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 814 Processing helix chain 'D' and resid 923 through 925 No H-bonds generated for 'chain 'D' and resid 923 through 925' Processing helix chain 'D' and resid 964 through 970 removed outlier: 3.748A pdb=" N MET D 968 " --> pdb=" O GLN D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1008 removed outlier: 3.636A pdb=" N PHE D1007 " --> pdb=" O SER D1004 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN D1008 " --> pdb=" O ALA D1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1004 through 1008' Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 86 removed outlier: 3.620A pdb=" N ASP A 82 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 60 " --> pdb=" O ASP A 82 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 56 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 149 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 159 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 89 removed outlier: 4.116A pdb=" N ILE A 208 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.939A pdb=" N ILE A 99 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 222 through 231 Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 273 removed outlier: 4.932A pdb=" N GLN A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN A 262 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 268 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 272 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 256 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 330 " --> pdb=" O TYR A 309 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 311 " --> pdb=" O CYS A 328 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS A 328 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A 324 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA8, first strand: chain 'A' and resid 484 through 485 removed outlier: 8.200A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL A 409 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP A 456 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 565 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 353 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 567 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU A 533 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY A 565 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 632 Processing sheet with id=AB1, first strand: chain 'A' and resid 661 through 669 removed outlier: 6.460A pdb=" N LEU A 658 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA A 664 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A 716 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 742 removed outlier: 3.525A pdb=" N ARG A 755 " --> pdb=" O TRP A 769 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A 767 " --> pdb=" O GLN A 757 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE A 770 " --> pdb=" O LYS A 773 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 781 through 783 removed outlier: 3.550A pdb=" N ARG A 781 " --> pdb=" O ASN A 885 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.647A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 14.310A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 21.655A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 24.943A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A1014 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 870 " --> pdb=" O TYR A1014 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 834 " --> pdb=" O ILE A 858 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 824 " --> pdb=" O ALA A 839 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA A 841 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU A 822 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN A 843 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA A 820 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 781 through 783 removed outlier: 3.550A pdb=" N ARG A 781 " --> pdb=" O ASN A 885 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.647A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 946 " --> pdb=" O HIS A 949 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY A 953 " --> pdb=" O ARG A 942 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY A 940 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 900 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 898 " --> pdb=" O ARG A 942 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU A 944 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN A 896 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N TYR A 946 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ARG A 894 " --> pdb=" O TYR A 946 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 920 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TRP A 897 " --> pdb=" O TRP A 918 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP A 918 " --> pdb=" O TRP A 897 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY A 899 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 901 " --> pdb=" O CYS A 914 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS A 914 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AB6, first strand: chain 'B' and resid 82 through 86 removed outlier: 3.620A pdb=" N ASP B 82 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE B 60 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 56 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA B 149 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 159 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 88 through 89 removed outlier: 4.117A pdb=" N ILE B 208 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.940A pdb=" N ILE B 99 " --> pdb=" O ARG B 204 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 222 through 231 Processing sheet with id=AC1, first strand: chain 'B' and resid 265 through 273 removed outlier: 4.932A pdb=" N GLN B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN B 262 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B 268 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 272 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 256 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 330 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 311 " --> pdb=" O CYS B 328 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS B 328 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 324 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AC3, first strand: chain 'B' and resid 484 through 485 removed outlier: 8.200A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N VAL B 409 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP B 456 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY B 565 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 353 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 567 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU B 533 " --> pdb=" O GLN B 563 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY B 565 " --> pdb=" O LEU B 533 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 627 through 632 Processing sheet with id=AC5, first strand: chain 'B' and resid 661 through 669 removed outlier: 6.460A pdb=" N LEU B 658 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA B 664 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA B 716 " --> pdb=" O VAL B 700 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 739 through 742 removed outlier: 3.524A pdb=" N ARG B 755 " --> pdb=" O TRP B 769 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 767 " --> pdb=" O GLN B 757 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 770 " --> pdb=" O LYS B 773 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 781 through 783 removed outlier: 3.550A pdb=" N ARG B 781 " --> pdb=" O ASN B 885 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.647A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.904A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 14.310A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 21.655A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 24.945A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR B1014 " --> pdb=" O VAL B 870 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 870 " --> pdb=" O TYR B1014 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 834 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 824 " --> pdb=" O ALA B 839 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA B 841 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU B 822 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN B 843 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA B 820 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 781 through 783 removed outlier: 3.550A pdb=" N ARG B 781 " --> pdb=" O ASN B 885 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.647A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B 946 " --> pdb=" O HIS B 949 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 953 " --> pdb=" O ARG B 942 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY B 940 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU B 900 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 898 " --> pdb=" O ARG B 942 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU B 944 " --> pdb=" O ASN B 896 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASN B 896 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N TYR B 946 " --> pdb=" O ARG B 894 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ARG B 894 " --> pdb=" O TYR B 946 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 920 " --> pdb=" O VAL B 895 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP B 897 " --> pdb=" O TRP B 918 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP B 918 " --> pdb=" O TRP B 897 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B 899 " --> pdb=" O ASP B 916 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 901 " --> pdb=" O CYS B 914 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS B 914 " --> pdb=" O GLY B 901 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AD1, first strand: chain 'C' and resid 82 through 86 removed outlier: 3.620A pdb=" N ASP C 82 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE C 60 " --> pdb=" O ASP C 82 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 56 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA C 149 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 159 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 88 through 89 removed outlier: 4.117A pdb=" N ILE C 208 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.940A pdb=" N ILE C 99 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 222 through 231 Processing sheet with id=AD5, first strand: chain 'C' and resid 265 through 273 removed outlier: 4.932A pdb=" N GLN C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN C 262 " --> pdb=" O GLN C 266 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C 268 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 272 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 256 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 330 " --> pdb=" O TYR C 309 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 311 " --> pdb=" O CYS C 328 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS C 328 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C 324 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AD7, first strand: chain 'C' and resid 484 through 485 removed outlier: 8.200A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL C 409 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TRP C 456 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY C 565 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 353 " --> pdb=" O GLY C 565 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 567 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU C 533 " --> pdb=" O GLN C 563 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY C 565 " --> pdb=" O LEU C 533 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 627 through 632 Processing sheet with id=AD9, first strand: chain 'C' and resid 661 through 669 removed outlier: 6.460A pdb=" N LEU C 658 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA C 664 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA C 716 " --> pdb=" O VAL C 700 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 739 through 742 removed outlier: 3.525A pdb=" N ARG C 755 " --> pdb=" O TRP C 769 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN C 767 " --> pdb=" O GLN C 757 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE C 770 " --> pdb=" O LYS C 773 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 781 through 783 removed outlier: 3.550A pdb=" N ARG C 781 " --> pdb=" O ASN C 885 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.646A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 14.310A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 21.656A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 24.944A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR C1014 " --> pdb=" O VAL C 870 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 870 " --> pdb=" O TYR C1014 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 834 " --> pdb=" O ILE C 858 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN C 824 " --> pdb=" O ALA C 839 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA C 841 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 822 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN C 843 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA C 820 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 781 through 783 removed outlier: 3.550A pdb=" N ARG C 781 " --> pdb=" O ASN C 885 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.646A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 946 " --> pdb=" O HIS C 949 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY C 953 " --> pdb=" O ARG C 942 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY C 940 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU C 900 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU C 898 " --> pdb=" O ARG C 942 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU C 944 " --> pdb=" O ASN C 896 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASN C 896 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR C 946 " --> pdb=" O ARG C 894 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ARG C 894 " --> pdb=" O TYR C 946 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 920 " --> pdb=" O VAL C 895 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP C 897 " --> pdb=" O TRP C 918 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP C 918 " --> pdb=" O TRP C 897 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY C 899 " --> pdb=" O ASP C 916 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY C 901 " --> pdb=" O CYS C 914 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS C 914 " --> pdb=" O GLY C 901 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AE5, first strand: chain 'D' and resid 82 through 86 removed outlier: 3.620A pdb=" N ASP D 82 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE D 60 " --> pdb=" O ASP D 82 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 56 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA D 149 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL D 159 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 88 through 89 removed outlier: 4.118A pdb=" N ILE D 208 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.939A pdb=" N ILE D 99 " --> pdb=" O ARG D 204 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 222 through 231 Processing sheet with id=AE9, first strand: chain 'D' and resid 265 through 273 removed outlier: 4.932A pdb=" N GLN D 266 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN D 262 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA D 268 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA D 272 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 256 " --> pdb=" O ALA D 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL D 330 " --> pdb=" O TYR D 309 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA D 311 " --> pdb=" O CYS D 328 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS D 328 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU D 324 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 335 through 337 Processing sheet with id=AF2, first strand: chain 'D' and resid 484 through 485 removed outlier: 8.201A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL D 409 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP D 456 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 565 " --> pdb=" O ILE D 351 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY D 353 " --> pdb=" O GLY D 565 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 567 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU D 533 " --> pdb=" O GLN D 563 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY D 565 " --> pdb=" O LEU D 533 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 627 through 632 Processing sheet with id=AF4, first strand: chain 'D' and resid 661 through 669 removed outlier: 6.459A pdb=" N LEU D 658 " --> pdb=" O PRO D 662 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA D 664 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA D 716 " --> pdb=" O VAL D 700 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 739 through 742 removed outlier: 3.524A pdb=" N ARG D 755 " --> pdb=" O TRP D 769 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 767 " --> pdb=" O GLN D 757 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE D 770 " --> pdb=" O LYS D 773 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 781 through 783 removed outlier: 3.550A pdb=" N ARG D 781 " --> pdb=" O ASN D 885 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.647A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 14.310A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 21.657A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 24.943A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR D1014 " --> pdb=" O VAL D 870 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL D 870 " --> pdb=" O TYR D1014 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 834 " --> pdb=" O ILE D 858 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN D 824 " --> pdb=" O ALA D 839 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA D 841 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU D 822 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN D 843 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALA D 820 " --> pdb=" O GLN D 843 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 781 through 783 removed outlier: 3.550A pdb=" N ARG D 781 " --> pdb=" O ASN D 885 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.647A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR D 946 " --> pdb=" O HIS D 949 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY D 953 " --> pdb=" O ARG D 942 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY D 940 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU D 900 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU D 898 " --> pdb=" O ARG D 942 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU D 944 " --> pdb=" O ASN D 896 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASN D 896 " --> pdb=" O LEU D 944 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR D 946 " --> pdb=" O ARG D 894 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ARG D 894 " --> pdb=" O TYR D 946 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 920 " --> pdb=" O VAL D 895 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TRP D 897 " --> pdb=" O TRP D 918 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP D 918 " --> pdb=" O TRP D 897 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY D 899 " --> pdb=" O ASP D 916 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY D 901 " --> pdb=" O CYS D 914 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS D 914 " --> pdb=" O GLY D 901 " (cutoff:3.500A) 920 hydrogen bonds defined for protein. 2448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.66 Time building geometry restraints manager: 3.75 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: 10711 1.34 - 1.45: 6204 1.45 - 1.57: 16629 1.57 - 1.69: 0 1.69 - 1.81: 248 Bond restraints: 33792 Sorted by residual: bond pdb=" CB TRP B 720 " pdb=" CG TRP B 720 " ideal model delta sigma weight residual 1.498 1.427 0.071 3.10e-02 1.04e+03 5.19e+00 bond pdb=" CB TRP D 720 " pdb=" CG TRP D 720 " ideal model delta sigma weight residual 1.498 1.428 0.070 3.10e-02 1.04e+03 5.17e+00 bond pdb=" CB TRP C 720 " pdb=" CG TRP C 720 " ideal model delta sigma weight residual 1.498 1.428 0.070 3.10e-02 1.04e+03 5.14e+00 bond pdb=" CB TRP A 720 " pdb=" CG TRP A 720 " ideal model delta sigma weight residual 1.498 1.428 0.070 3.10e-02 1.04e+03 5.14e+00 bond pdb=" CA ASP A 610 " pdb=" C ASP A 610 " ideal model delta sigma weight residual 1.523 1.540 -0.016 8.40e-03 1.42e+04 3.77e+00 ... (remaining 33787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 44368 2.43 - 4.86: 1532 4.86 - 7.29: 160 7.29 - 9.71: 33 9.71 - 12.14: 11 Bond angle restraints: 46104 Sorted by residual: angle pdb=" C GLY C 771 " pdb=" N ASP C 772 " pdb=" CA ASP C 772 " ideal model delta sigma weight residual 121.70 133.84 -12.14 1.80e+00 3.09e-01 4.55e+01 angle pdb=" C GLY B 771 " pdb=" N ASP B 772 " pdb=" CA ASP B 772 " ideal model delta sigma weight residual 121.70 133.84 -12.14 1.80e+00 3.09e-01 4.55e+01 angle pdb=" C GLY D 771 " pdb=" N ASP D 772 " pdb=" CA ASP D 772 " ideal model delta sigma weight residual 121.70 133.82 -12.12 1.80e+00 3.09e-01 4.53e+01 angle pdb=" C GLY A 771 " pdb=" N ASP A 772 " pdb=" CA ASP A 772 " ideal model delta sigma weight residual 121.70 133.81 -12.11 1.80e+00 3.09e-01 4.53e+01 angle pdb=" C ASP C 610 " pdb=" N ARG C 611 " pdb=" CA ARG C 611 " ideal model delta sigma weight residual 121.70 132.46 -10.76 1.80e+00 3.09e-01 3.58e+01 ... (remaining 46099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.40: 18526 15.40 - 30.80: 1003 30.80 - 46.20: 231 46.20 - 61.60: 4 61.60 - 77.00: 36 Dihedral angle restraints: 19800 sinusoidal: 7984 harmonic: 11816 Sorted by residual: dihedral pdb=" CA TRP B 769 " pdb=" C TRP B 769 " pdb=" N ILE B 770 " pdb=" CA ILE B 770 " ideal model delta harmonic sigma weight residual 180.00 149.17 30.83 0 5.00e+00 4.00e-02 3.80e+01 dihedral pdb=" CA TRP C 769 " pdb=" C TRP C 769 " pdb=" N ILE C 770 " pdb=" CA ILE C 770 " ideal model delta harmonic sigma weight residual 180.00 149.17 30.83 0 5.00e+00 4.00e-02 3.80e+01 dihedral pdb=" CA TRP D 769 " pdb=" C TRP D 769 " pdb=" N ILE D 770 " pdb=" CA ILE D 770 " ideal model delta harmonic sigma weight residual 180.00 149.18 30.82 0 5.00e+00 4.00e-02 3.80e+01 ... (remaining 19797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3033 0.054 - 0.109: 1401 0.109 - 0.163: 317 0.163 - 0.217: 49 0.217 - 0.272: 20 Chirality restraints: 4820 Sorted by residual: chirality pdb=" CB ILE C 737 " pdb=" CA ILE C 737 " pdb=" CG1 ILE C 737 " pdb=" CG2 ILE C 737 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE D 737 " pdb=" CA ILE D 737 " pdb=" CG1 ILE D 737 " pdb=" CG2 ILE D 737 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE A 737 " pdb=" CA ILE A 737 " pdb=" CG1 ILE A 737 " pdb=" CG2 ILE A 737 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 4817 not shown) Planarity restraints: 6088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 58 " -0.026 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP A 58 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP A 58 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 58 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 58 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 58 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 58 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 58 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 58 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 58 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 58 " -0.026 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP C 58 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP C 58 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C 58 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 58 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 58 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 58 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 58 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 58 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP C 58 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 58 " 0.026 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP B 58 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP B 58 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 58 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 58 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 58 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 58 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 58 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 58 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 58 " -0.001 2.00e-02 2.50e+03 ... (remaining 6085 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 4099 2.74 - 3.28: 26977 3.28 - 3.82: 48988 3.82 - 4.36: 53552 4.36 - 4.90: 96460 Nonbonded interactions: 230076 Sorted by model distance: nonbonded pdb=" ND1 HIS B 418 " pdb="MG MG B3001 " model vdw 2.206 2.250 nonbonded pdb=" ND1 HIS A 418 " pdb="MG MG A3001 " model vdw 2.211 2.250 nonbonded pdb=" ND1 HIS C 418 " pdb="MG MG C3001 " model vdw 2.213 2.250 nonbonded pdb=" ND1 HIS D 418 " pdb="MG MG D3001 " model vdw 2.224 2.250 nonbonded pdb=" OH TYR A 906 " pdb=" OE1 GLU A 934 " model vdw 2.251 3.040 ... (remaining 230071 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: 0.10 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 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: 0.330 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 34.510 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 0.075 33792 Z= 0.378 Angle : 1.046 12.143 46104 Z= 0.591 Chirality : 0.063 0.272 4820 Planarity : 0.008 0.067 6088 Dihedral : 10.751 76.997 12192 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.57 % Favored : 93.33 % Rotamer: Outliers : 0.34 % Allowed : 3.55 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.48 (0.11), residues: 4080 helix: -4.73 (0.10), residues: 340 sheet: -0.73 (0.14), residues: 1244 loop : -2.97 (0.10), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 166 TYR 0.029 0.003 TYR A 538 PHE 0.024 0.004 PHE C 989 TRP 0.056 0.004 TRP A 58 HIS 0.014 0.003 HIS B 972 Details of bonding type rmsd covalent geometry : bond 0.00839 (33792) covalent geometry : angle 1.04624 (46104) hydrogen bonds : bond 0.16498 ( 856) hydrogen bonds : angle 9.32366 ( 2448) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1046 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8492 (t) cc_final: 0.8216 (m) REVERT: A 23 GLN cc_start: 0.7797 (pp30) cc_final: 0.7324 (pp30) REVERT: A 62 TRP cc_start: 0.8361 (t60) cc_final: 0.7814 (t60) REVERT: A 75 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7421 (tm-30) REVERT: A 84 VAL cc_start: 0.7952 (t) cc_final: 0.7374 (p) REVERT: A 85 VAL cc_start: 0.8682 (t) cc_final: 0.8462 (p) REVERT: A 92 MET cc_start: 0.8434 (mmm) cc_final: 0.7937 (mmm) REVERT: A 100 TYR cc_start: 0.7333 (t80) cc_final: 0.6544 (t80) REVERT: A 132 SER cc_start: 0.8826 (m) cc_final: 0.8150 (t) REVERT: A 144 ASP cc_start: 0.8066 (m-30) cc_final: 0.7774 (t0) REVERT: A 187 MET cc_start: 0.8317 (ttp) cc_final: 0.8107 (ttp) REVERT: A 233 ASP cc_start: 0.7744 (p0) cc_final: 0.7498 (p0) REVERT: A 243 GLU cc_start: 0.7327 (tt0) cc_final: 0.6292 (pp20) REVERT: A 288 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7524 (mtt-85) REVERT: A 416 GLU cc_start: 0.6834 (tt0) cc_final: 0.6521 (tt0) REVERT: A 443 MET cc_start: 0.7713 (ttp) cc_final: 0.7482 (ttm) REVERT: A 515 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8405 (m) REVERT: A 518 TRP cc_start: 0.8512 (m100) cc_final: 0.8126 (m100) REVERT: A 585 TRP cc_start: 0.8700 (p-90) cc_final: 0.8045 (p-90) REVERT: A 601 PHE cc_start: 0.8483 (m-80) cc_final: 0.8245 (m-80) REVERT: A 634 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8444 (mm110) REVERT: A 637 GLU cc_start: 0.7197 (tt0) cc_final: 0.6929 (tt0) REVERT: A 655 MET cc_start: 0.7894 (ttt) cc_final: 0.7601 (ttm) REVERT: A 670 LEU cc_start: 0.8333 (tt) cc_final: 0.8108 (tp) REVERT: A 672 VAL cc_start: 0.8506 (m) cc_final: 0.7998 (t) REVERT: A 677 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7897 (mtpt) REVERT: A 693 GLN cc_start: 0.7028 (tp40) cc_final: 0.6751 (tp40) REVERT: A 699 ARG cc_start: 0.7091 (ptp-110) cc_final: 0.6806 (ptp90) REVERT: A 708 TRP cc_start: 0.8385 (p-90) cc_final: 0.8050 (p-90) REVERT: A 709 SER cc_start: 0.8333 (t) cc_final: 0.7929 (p) REVERT: A 773 LYS cc_start: 0.7335 (tmmt) cc_final: 0.6865 (tmmt) REVERT: A 777 LEU cc_start: 0.8044 (mt) cc_final: 0.7815 (mp) REVERT: A 792 ASP cc_start: 0.8150 (p0) cc_final: 0.7769 (p0) REVERT: A 853 ARG cc_start: 0.7161 (mtt90) cc_final: 0.6626 (mtt90) REVERT: A 888 LEU cc_start: 0.7751 (mt) cc_final: 0.7513 (mt) REVERT: A 898 LEU cc_start: 0.6957 (tp) cc_final: 0.6174 (tp) REVERT: A 925 MET cc_start: 0.8128 (mmm) cc_final: 0.7663 (mmt) REVERT: A 955 PHE cc_start: 0.8580 (p90) cc_final: 0.8229 (p90) REVERT: A 974 HIS cc_start: 0.7714 (p-80) cc_final: 0.7311 (p-80) REVERT: A 975 LEU cc_start: 0.8744 (mt) cc_final: 0.8197 (mt) REVERT: A 1019 VAL cc_start: 0.8344 (t) cc_final: 0.7794 (p) REVERT: B 18 ASN cc_start: 0.8742 (t0) cc_final: 0.8224 (t0) REVERT: B 40 GLU cc_start: 0.7929 (tt0) cc_final: 0.7551 (tp30) REVERT: B 62 TRP cc_start: 0.8342 (t60) cc_final: 0.7783 (t60) REVERT: B 75 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7792 (tm-30) REVERT: B 84 VAL cc_start: 0.8107 (t) cc_final: 0.7534 (p) REVERT: B 85 VAL cc_start: 0.8676 (t) cc_final: 0.8447 (p) REVERT: B 92 MET cc_start: 0.8523 (mmm) cc_final: 0.7986 (mmm) REVERT: B 131 GLU cc_start: 0.7489 (tt0) cc_final: 0.7219 (tp30) REVERT: B 132 SER cc_start: 0.8753 (m) cc_final: 0.8411 (t) REVERT: B 144 ASP cc_start: 0.8242 (m-30) cc_final: 0.7834 (m-30) REVERT: B 161 TYR cc_start: 0.7853 (t80) cc_final: 0.7456 (t80) REVERT: B 187 MET cc_start: 0.8503 (ttp) cc_final: 0.8295 (ttp) REVERT: B 202 MET cc_start: 0.8005 (ptt) cc_final: 0.7747 (ptm) REVERT: B 211 ASP cc_start: 0.7630 (t0) cc_final: 0.7390 (t0) REVERT: B 299 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7569 (mtpp) REVERT: B 307 ASN cc_start: 0.8545 (m-40) cc_final: 0.8334 (m-40) REVERT: B 411 ASP cc_start: 0.7611 (t0) cc_final: 0.7371 (t70) REVERT: B 443 MET cc_start: 0.7874 (ttp) cc_final: 0.7591 (ttm) REVERT: B 487 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7467 (tm-30) REVERT: B 518 TRP cc_start: 0.8599 (m100) cc_final: 0.8148 (m100) REVERT: B 544 ASN cc_start: 0.8355 (m-40) cc_final: 0.7995 (m-40) REVERT: B 570 TRP cc_start: 0.7723 (t-100) cc_final: 0.7308 (t-100) REVERT: B 585 TRP cc_start: 0.8516 (p-90) cc_final: 0.7746 (p-90) REVERT: B 603 MET cc_start: 0.7098 (mmt) cc_final: 0.6493 (mmt) REVERT: B 625 GLN cc_start: 0.7833 (pt0) cc_final: 0.7575 (pt0) REVERT: B 634 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8577 (mm110) REVERT: B 637 GLU cc_start: 0.7150 (tt0) cc_final: 0.6928 (tt0) REVERT: B 647 SER cc_start: 0.7835 (t) cc_final: 0.7607 (t) REVERT: B 655 MET cc_start: 0.7795 (ttt) cc_final: 0.7516 (ttm) REVERT: B 670 LEU cc_start: 0.8147 (tt) cc_final: 0.7898 (tp) REVERT: B 672 VAL cc_start: 0.8538 (m) cc_final: 0.8197 (t) REVERT: B 677 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8038 (mtpp) REVERT: B 693 GLN cc_start: 0.7005 (tp40) cc_final: 0.6687 (tp40) REVERT: B 699 ARG cc_start: 0.7212 (ptp-110) cc_final: 0.6811 (ptp-170) REVERT: B 708 TRP cc_start: 0.8305 (p-90) cc_final: 0.7972 (p-90) REVERT: B 792 ASP cc_start: 0.8327 (p0) cc_final: 0.7994 (p0) REVERT: B 837 THR cc_start: 0.7530 (p) cc_final: 0.7245 (t) REVERT: B 852 SER cc_start: 0.8687 (t) cc_final: 0.8377 (p) REVERT: B 853 ARG cc_start: 0.7403 (mtt90) cc_final: 0.6946 (mtt90) REVERT: B 868 VAL cc_start: 0.8424 (t) cc_final: 0.8136 (t) REVERT: B 871 GLU cc_start: 0.6634 (tt0) cc_final: 0.6313 (mt-10) REVERT: B 890 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7541 (mm-40) REVERT: B 898 LEU cc_start: 0.6605 (tp) cc_final: 0.5778 (tp) REVERT: B 905 ASN cc_start: 0.7227 (p0) cc_final: 0.6825 (p0) REVERT: B 906 TYR cc_start: 0.7196 (m-10) cc_final: 0.6726 (m-10) REVERT: B 931 PHE cc_start: 0.7006 (t80) cc_final: 0.6778 (t80) REVERT: B 955 PHE cc_start: 0.8464 (p90) cc_final: 0.8179 (p90) REVERT: B 974 HIS cc_start: 0.7605 (p-80) cc_final: 0.7234 (p-80) REVERT: B 975 LEU cc_start: 0.8633 (mt) cc_final: 0.8240 (mt) REVERT: B 1016 TYR cc_start: 0.7870 (p90) cc_final: 0.7661 (p90) REVERT: B 1019 VAL cc_start: 0.8391 (t) cc_final: 0.7904 (p) REVERT: C 10 VAL cc_start: 0.8348 (t) cc_final: 0.7952 (m) REVERT: C 46 ARG cc_start: 0.8024 (mtt180) cc_final: 0.7800 (ttm110) REVERT: C 62 TRP cc_start: 0.8508 (t60) cc_final: 0.7879 (t60) REVERT: C 84 VAL cc_start: 0.8158 (t) cc_final: 0.7603 (p) REVERT: C 85 VAL cc_start: 0.8803 (t) cc_final: 0.8553 (p) REVERT: C 92 MET cc_start: 0.8432 (mmm) cc_final: 0.7928 (mmm) REVERT: C 131 GLU cc_start: 0.7176 (tt0) cc_final: 0.6850 (tp30) REVERT: C 132 SER cc_start: 0.8873 (m) cc_final: 0.8474 (t) REVERT: C 144 ASP cc_start: 0.8215 (m-30) cc_final: 0.7595 (t0) REVERT: C 161 TYR cc_start: 0.7921 (t80) cc_final: 0.7429 (t80) REVERT: C 187 MET cc_start: 0.8367 (ttp) cc_final: 0.8109 (ttp) REVERT: C 288 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7205 (mtt-85) REVERT: C 372 MET cc_start: 0.7600 (mtt) cc_final: 0.7379 (mtm) REVERT: C 443 MET cc_start: 0.7734 (ttp) cc_final: 0.7438 (ttm) REVERT: C 492 ASP cc_start: 0.7771 (t0) cc_final: 0.7425 (t0) REVERT: C 515 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8189 (m) REVERT: C 518 TRP cc_start: 0.8376 (m100) cc_final: 0.7885 (m100) REVERT: C 585 TRP cc_start: 0.8599 (p-90) cc_final: 0.7993 (p-90) REVERT: C 603 MET cc_start: 0.6996 (mmt) cc_final: 0.6505 (mmt) REVERT: C 634 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8563 (mm110) REVERT: C 637 GLU cc_start: 0.7171 (tt0) cc_final: 0.6939 (tt0) REVERT: C 647 SER cc_start: 0.8050 (t) cc_final: 0.7826 (t) REVERT: C 655 MET cc_start: 0.7865 (ttt) cc_final: 0.7629 (ttm) REVERT: C 670 LEU cc_start: 0.8192 (tt) cc_final: 0.7897 (tp) REVERT: C 672 VAL cc_start: 0.8601 (m) cc_final: 0.8184 (t) REVERT: C 677 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7942 (mtpt) REVERT: C 687 GLN cc_start: 0.7906 (pt0) cc_final: 0.7571 (pm20) REVERT: C 693 GLN cc_start: 0.7063 (tp40) cc_final: 0.6816 (tp40) REVERT: C 708 TRP cc_start: 0.8339 (p-90) cc_final: 0.7887 (p-90) REVERT: C 739 HIS cc_start: 0.7110 (t70) cc_final: 0.6619 (t70) REVERT: C 773 LYS cc_start: 0.7379 (tmmt) cc_final: 0.6999 (tmmt) REVERT: C 792 ASP cc_start: 0.8303 (p0) cc_final: 0.7839 (p0) REVERT: C 808 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7399 (mm-30) REVERT: C 837 THR cc_start: 0.7750 (p) cc_final: 0.7502 (t) REVERT: C 853 ARG cc_start: 0.7629 (mtt90) cc_final: 0.7191 (mtt90) REVERT: C 898 LEU cc_start: 0.7002 (tp) cc_final: 0.6281 (tp) REVERT: C 924 ASP cc_start: 0.8523 (m-30) cc_final: 0.7998 (t0) REVERT: C 942 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.8088 (tpp80) REVERT: C 955 PHE cc_start: 0.8552 (p90) cc_final: 0.8197 (p90) REVERT: C 974 HIS cc_start: 0.7674 (p-80) cc_final: 0.7317 (p-80) REVERT: C 975 LEU cc_start: 0.8557 (mt) cc_final: 0.8031 (mt) REVERT: C 1019 VAL cc_start: 0.8363 (t) cc_final: 0.7864 (p) REVERT: D 10 VAL cc_start: 0.8432 (t) cc_final: 0.8214 (m) REVERT: D 62 TRP cc_start: 0.8378 (t60) cc_final: 0.7807 (t60) REVERT: D 67 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7443 (mp0) REVERT: D 75 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7661 (tm-30) REVERT: D 84 VAL cc_start: 0.8077 (t) cc_final: 0.7542 (p) REVERT: D 85 VAL cc_start: 0.8610 (t) cc_final: 0.8358 (p) REVERT: D 92 MET cc_start: 0.8521 (mmm) cc_final: 0.7999 (mmm) REVERT: D 132 SER cc_start: 0.8762 (m) cc_final: 0.8431 (t) REVERT: D 161 TYR cc_start: 0.7939 (t80) cc_final: 0.7717 (t80) REVERT: D 170 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6749 (pm20) REVERT: D 187 MET cc_start: 0.8561 (ttp) cc_final: 0.8230 (ttp) REVERT: D 202 MET cc_start: 0.7998 (ptt) cc_final: 0.7683 (ptp) REVERT: D 243 GLU cc_start: 0.7135 (tt0) cc_final: 0.6584 (pp20) REVERT: D 255 ARG cc_start: 0.7693 (mmt90) cc_final: 0.7415 (mmt-90) REVERT: D 370 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8371 (mm110) REVERT: D 429 ASP cc_start: 0.8453 (t70) cc_final: 0.8196 (t0) REVERT: D 443 MET cc_start: 0.7909 (ttp) cc_final: 0.7649 (ttm) REVERT: D 487 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7529 (tm-30) REVERT: D 518 TRP cc_start: 0.8522 (m100) cc_final: 0.8111 (m100) REVERT: D 585 TRP cc_start: 0.8583 (p-90) cc_final: 0.8011 (p-90) REVERT: D 603 MET cc_start: 0.7085 (mmt) cc_final: 0.6262 (mmt) REVERT: D 634 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8560 (mm-40) REVERT: D 655 MET cc_start: 0.7854 (ttt) cc_final: 0.7600 (ttm) REVERT: D 659 ASP cc_start: 0.8341 (t0) cc_final: 0.7617 (p0) REVERT: D 670 LEU cc_start: 0.8293 (tt) cc_final: 0.8016 (tp) REVERT: D 672 VAL cc_start: 0.8683 (m) cc_final: 0.8376 (t) REVERT: D 677 LYS cc_start: 0.8518 (mtpt) cc_final: 0.7984 (mtpt) REVERT: D 693 GLN cc_start: 0.7043 (tp40) cc_final: 0.6761 (tp40) REVERT: D 699 ARG cc_start: 0.7034 (ptp-110) cc_final: 0.6796 (ptp-170) REVERT: D 708 TRP cc_start: 0.8388 (p-90) cc_final: 0.8123 (p-90) REVERT: D 709 SER cc_start: 0.8516 (t) cc_final: 0.7885 (p) REVERT: D 773 LYS cc_start: 0.7020 (tmmt) cc_final: 0.6787 (tmmt) REVERT: D 777 LEU cc_start: 0.7733 (mt) cc_final: 0.7452 (mp) REVERT: D 781 ARG cc_start: 0.6678 (ttt90) cc_final: 0.6417 (ttm110) REVERT: D 792 ASP cc_start: 0.8201 (p0) cc_final: 0.7996 (p0) REVERT: D 799 THR cc_start: 0.8782 (m) cc_final: 0.8251 (p) REVERT: D 844 HIS cc_start: 0.7342 (t-90) cc_final: 0.6668 (t70) REVERT: D 853 ARG cc_start: 0.7810 (mtt90) cc_final: 0.7401 (mtt90) REVERT: D 898 LEU cc_start: 0.7014 (tp) cc_final: 0.6228 (tp) REVERT: D 924 ASP cc_start: 0.8357 (m-30) cc_final: 0.7804 (t0) REVERT: D 925 MET cc_start: 0.8127 (mmm) cc_final: 0.7847 (mmt) REVERT: D 997 ASP cc_start: 0.7561 (m-30) cc_final: 0.7324 (m-30) REVERT: D 1007 PHE cc_start: 0.8401 (m-10) cc_final: 0.8009 (m-10) REVERT: D 1016 TYR cc_start: 0.7884 (p90) cc_final: 0.7608 (p90) REVERT: D 1019 VAL cc_start: 0.8441 (t) cc_final: 0.7974 (p) outliers start: 12 outliers final: 2 residues processed: 1058 average time/residue: 0.2375 time to fit residues: 389.0305 Evaluate side-chains 861 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 857 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 884 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.0050 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 30 HIS A 155 ASN A 163 GLN A 382 ASN A 468 HIS A 604 ASN A 628 GLN A 719 GLN A 725 ASN A 775 GLN A 824 GLN A 890 GLN A 990 HIS B 25 ASN B 30 HIS B 155 ASN B 163 GLN B 382 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 ASN B 628 GLN B 775 GLN B 844 HIS B 890 GLN B 990 HIS C 25 ASN C 30 HIS C 155 ASN C 163 GLN C 382 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS C 604 ASN C 628 GLN C 725 ASN ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN D 30 HIS D 155 ASN D 163 GLN D 216 HIS D 382 ASN ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 ASN D 628 GLN D 719 GLN D 775 GLN D 990 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.097123 restraints weight = 57691.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.100470 restraints weight = 27095.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.102658 restraints weight = 15571.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104127 restraints weight = 10477.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104942 restraints weight = 7925.897| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33792 Z= 0.177 Angle : 0.687 8.270 46104 Z= 0.363 Chirality : 0.047 0.184 4820 Planarity : 0.005 0.051 6088 Dihedral : 5.694 37.524 4478 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.43 % Allowed : 10.90 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.91 (0.12), residues: 4080 helix: -3.56 (0.19), residues: 356 sheet: -0.47 (0.14), residues: 1352 loop : -2.69 (0.11), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 630 TYR 0.018 0.002 TYR C 538 PHE 0.018 0.002 PHE C 989 TRP 0.024 0.002 TRP A 58 HIS 0.009 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00409 (33792) covalent geometry : angle 0.68707 (46104) hydrogen bonds : bond 0.05051 ( 856) hydrogen bonds : angle 6.52138 ( 2448) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 860 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TRP cc_start: 0.8134 (t60) cc_final: 0.7667 (t60) REVERT: A 67 GLU cc_start: 0.7577 (mp0) cc_final: 0.7291 (mp0) REVERT: A 75 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 84 VAL cc_start: 0.8113 (t) cc_final: 0.7557 (p) REVERT: A 85 VAL cc_start: 0.8718 (t) cc_final: 0.8458 (p) REVERT: A 92 MET cc_start: 0.8323 (mmm) cc_final: 0.7882 (mmm) REVERT: A 100 TYR cc_start: 0.7049 (t80) cc_final: 0.6318 (t80) REVERT: A 144 ASP cc_start: 0.7927 (m-30) cc_final: 0.7643 (t0) REVERT: A 161 TYR cc_start: 0.7900 (t80) cc_final: 0.7582 (t80) REVERT: A 187 MET cc_start: 0.8312 (ttp) cc_final: 0.8106 (ttp) REVERT: A 233 ASP cc_start: 0.7528 (p0) cc_final: 0.7257 (p0) REVERT: A 243 GLU cc_start: 0.7125 (tt0) cc_final: 0.6744 (tt0) REVERT: A 403 ASP cc_start: 0.7335 (m-30) cc_final: 0.6890 (m-30) REVERT: A 492 ASP cc_start: 0.7748 (t0) cc_final: 0.7271 (t0) REVERT: A 515 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8263 (m) REVERT: A 518 TRP cc_start: 0.8570 (m100) cc_final: 0.8154 (m100) REVERT: A 553 TRP cc_start: 0.8272 (m100) cc_final: 0.7902 (m100) REVERT: A 585 TRP cc_start: 0.8757 (p-90) cc_final: 0.7870 (p-90) REVERT: A 599 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.5360 (pmt-80) REVERT: A 601 PHE cc_start: 0.8367 (m-80) cc_final: 0.8161 (m-80) REVERT: A 634 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8435 (mm-40) REVERT: A 637 GLU cc_start: 0.7091 (tt0) cc_final: 0.6631 (tt0) REVERT: A 655 MET cc_start: 0.7921 (ttt) cc_final: 0.7641 (ttm) REVERT: A 677 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7772 (mtpt) REVERT: A 709 SER cc_start: 0.8377 (t) cc_final: 0.7862 (p) REVERT: A 773 LYS cc_start: 0.7297 (tmmt) cc_final: 0.7000 (tmmt) REVERT: A 777 LEU cc_start: 0.7987 (mt) cc_final: 0.7754 (mp) REVERT: A 792 ASP cc_start: 0.7857 (p0) cc_final: 0.7550 (p0) REVERT: A 853 ARG cc_start: 0.7319 (mtt90) cc_final: 0.6941 (mtt90) REVERT: A 935 ASN cc_start: 0.8928 (p0) cc_final: 0.8551 (p0) REVERT: A 955 PHE cc_start: 0.8392 (p90) cc_final: 0.7911 (p90) REVERT: A 974 HIS cc_start: 0.7661 (p-80) cc_final: 0.7240 (p-80) REVERT: A 975 LEU cc_start: 0.8635 (mt) cc_final: 0.8157 (mt) REVERT: A 997 ASP cc_start: 0.7299 (m-30) cc_final: 0.7057 (t0) REVERT: A 1019 VAL cc_start: 0.8355 (t) cc_final: 0.7832 (p) REVERT: B 9 VAL cc_start: 0.9270 (m) cc_final: 0.8994 (p) REVERT: B 62 TRP cc_start: 0.8129 (t60) cc_final: 0.7788 (t60) REVERT: B 67 GLU cc_start: 0.7520 (mp0) cc_final: 0.7279 (mp0) REVERT: B 84 VAL cc_start: 0.8248 (t) cc_final: 0.7694 (p) REVERT: B 85 VAL cc_start: 0.8705 (t) cc_final: 0.8437 (p) REVERT: B 90 TRP cc_start: 0.7741 (p90) cc_final: 0.7156 (p90) REVERT: B 92 MET cc_start: 0.8517 (mmm) cc_final: 0.8046 (mmm) REVERT: B 100 TYR cc_start: 0.7113 (t80) cc_final: 0.6573 (t80) REVERT: B 144 ASP cc_start: 0.8151 (m-30) cc_final: 0.7605 (m-30) REVERT: B 161 TYR cc_start: 0.7923 (t80) cc_final: 0.7284 (t80) REVERT: B 167 LEU cc_start: 0.7493 (mt) cc_final: 0.7230 (mp) REVERT: B 211 ASP cc_start: 0.7587 (t0) cc_final: 0.7282 (t0) REVERT: B 237 ARG cc_start: 0.7334 (mtp85) cc_final: 0.6998 (mtp85) REVERT: B 288 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.7478 (mtt-85) REVERT: B 299 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7479 (mtpp) REVERT: B 338 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7380 (tm-30) REVERT: B 403 ASP cc_start: 0.7303 (m-30) cc_final: 0.6829 (m-30) REVERT: B 411 ASP cc_start: 0.7370 (t0) cc_final: 0.7042 (m-30) REVERT: B 443 MET cc_start: 0.7854 (ttp) cc_final: 0.7337 (ttp) REVERT: B 492 ASP cc_start: 0.7764 (t0) cc_final: 0.7283 (t0) REVERT: B 544 ASN cc_start: 0.8450 (m-40) cc_final: 0.8193 (m-40) REVERT: B 570 TRP cc_start: 0.7775 (t-100) cc_final: 0.7341 (t-100) REVERT: B 585 TRP cc_start: 0.8637 (p-90) cc_final: 0.7319 (p-90) REVERT: B 599 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.5352 (pmt-80) REVERT: B 603 MET cc_start: 0.6988 (mmt) cc_final: 0.6430 (mmt) REVERT: B 634 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8533 (mm110) REVERT: B 637 GLU cc_start: 0.7206 (tt0) cc_final: 0.6905 (tt0) REVERT: B 655 MET cc_start: 0.7782 (ttt) cc_final: 0.7531 (ttm) REVERT: B 667 GLU cc_start: 0.7208 (pm20) cc_final: 0.6698 (pm20) REVERT: B 672 VAL cc_start: 0.8569 (m) cc_final: 0.8343 (t) REVERT: B 677 LYS cc_start: 0.8499 (mtpt) cc_final: 0.7962 (mtpp) REVERT: B 693 GLN cc_start: 0.6989 (tp40) cc_final: 0.5710 (tp40) REVERT: B 708 TRP cc_start: 0.8243 (p-90) cc_final: 0.7955 (p-90) REVERT: B 709 SER cc_start: 0.8282 (t) cc_final: 0.7828 (p) REVERT: B 721 ARG cc_start: 0.7443 (mtp180) cc_final: 0.7080 (mtp-110) REVERT: B 749 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7133 (tp) REVERT: B 756 TRP cc_start: 0.7538 (m-90) cc_final: 0.7136 (m-90) REVERT: B 777 LEU cc_start: 0.7551 (mt) cc_final: 0.7335 (mp) REVERT: B 808 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7422 (mm-30) REVERT: B 896 ASN cc_start: 0.7719 (t0) cc_final: 0.7511 (t0) REVERT: B 898 LEU cc_start: 0.6376 (tp) cc_final: 0.6173 (tp) REVERT: B 906 TYR cc_start: 0.7393 (m-10) cc_final: 0.7124 (m-10) REVERT: B 919 ASP cc_start: 0.8048 (m-30) cc_final: 0.7687 (t0) REVERT: B 955 PHE cc_start: 0.8317 (p90) cc_final: 0.7895 (p90) REVERT: B 974 HIS cc_start: 0.7419 (p-80) cc_final: 0.7092 (p90) REVERT: B 975 LEU cc_start: 0.8473 (mt) cc_final: 0.8103 (mt) REVERT: B 997 ASP cc_start: 0.7317 (m-30) cc_final: 0.7092 (m-30) REVERT: B 1018 LEU cc_start: 0.8628 (pp) cc_final: 0.8245 (mt) REVERT: B 1019 VAL cc_start: 0.8425 (t) cc_final: 0.7829 (p) REVERT: C 9 VAL cc_start: 0.9206 (m) cc_final: 0.8955 (p) REVERT: C 62 TRP cc_start: 0.8287 (t60) cc_final: 0.7935 (t60) REVERT: C 77 ASP cc_start: 0.7887 (m-30) cc_final: 0.7536 (m-30) REVERT: C 84 VAL cc_start: 0.8300 (t) cc_final: 0.7797 (p) REVERT: C 85 VAL cc_start: 0.8823 (t) cc_final: 0.8557 (p) REVERT: C 92 MET cc_start: 0.8394 (mmm) cc_final: 0.7941 (mmm) REVERT: C 100 TYR cc_start: 0.7384 (t80) cc_final: 0.6405 (t80) REVERT: C 124 SER cc_start: 0.7702 (m) cc_final: 0.7419 (p) REVERT: C 144 ASP cc_start: 0.8052 (m-30) cc_final: 0.7497 (m-30) REVERT: C 187 MET cc_start: 0.8382 (ttp) cc_final: 0.8091 (ttp) REVERT: C 211 ASP cc_start: 0.7913 (t0) cc_final: 0.7599 (m-30) REVERT: C 221 GLN cc_start: 0.8330 (pm20) cc_final: 0.7883 (pm20) REVERT: C 237 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.7315 (mtp85) REVERT: C 246 MET cc_start: 0.8204 (ppp) cc_final: 0.7976 (tmm) REVERT: C 299 LYS cc_start: 0.8239 (mmmm) cc_final: 0.7706 (mtpp) REVERT: C 349 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7556 (tp) REVERT: C 403 ASP cc_start: 0.7189 (m-30) cc_final: 0.6604 (m-30) REVERT: C 444 VAL cc_start: 0.7885 (t) cc_final: 0.7684 (p) REVERT: C 487 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7451 (tm-30) REVERT: C 492 ASP cc_start: 0.7737 (t0) cc_final: 0.7379 (t0) REVERT: C 515 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8067 (m) REVERT: C 518 TRP cc_start: 0.8470 (m100) cc_final: 0.8012 (m100) REVERT: C 585 TRP cc_start: 0.8668 (p-90) cc_final: 0.8011 (p-90) REVERT: C 599 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.5270 (pmt-80) REVERT: C 603 MET cc_start: 0.6911 (mmt) cc_final: 0.6526 (mmt) REVERT: C 634 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8443 (mm-40) REVERT: C 637 GLU cc_start: 0.7011 (tt0) cc_final: 0.6583 (tt0) REVERT: C 677 LYS cc_start: 0.8311 (mtpt) cc_final: 0.7804 (mtpt) REVERT: C 687 GLN cc_start: 0.7824 (pt0) cc_final: 0.7582 (pm20) REVERT: C 693 GLN cc_start: 0.7112 (tp40) cc_final: 0.6868 (tp40) REVERT: C 739 HIS cc_start: 0.7256 (t70) cc_final: 0.6999 (t70) REVERT: C 773 LYS cc_start: 0.7235 (tmmt) cc_final: 0.6914 (tmmt) REVERT: C 792 ASP cc_start: 0.7986 (p0) cc_final: 0.7672 (p0) REVERT: C 808 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7298 (mm-30) REVERT: C 837 THR cc_start: 0.8172 (p) cc_final: 0.7931 (t) REVERT: C 853 ARG cc_start: 0.7704 (mtt90) cc_final: 0.7470 (mtt90) REVERT: C 924 ASP cc_start: 0.8391 (m-30) cc_final: 0.8033 (t0) REVERT: C 942 ARG cc_start: 0.8242 (mmm-85) cc_final: 0.7988 (tpp80) REVERT: C 955 PHE cc_start: 0.8378 (p90) cc_final: 0.8083 (p90) REVERT: C 974 HIS cc_start: 0.7487 (p-80) cc_final: 0.7117 (p-80) REVERT: C 975 LEU cc_start: 0.8463 (mt) cc_final: 0.7982 (mt) REVERT: C 1019 VAL cc_start: 0.8384 (t) cc_final: 0.7902 (p) REVERT: D 46 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7906 (ttm-80) REVERT: D 62 TRP cc_start: 0.8116 (t60) cc_final: 0.7760 (t60) REVERT: D 67 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7392 (mp0) REVERT: D 75 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7531 (tm-30) REVERT: D 84 VAL cc_start: 0.8239 (t) cc_final: 0.7697 (p) REVERT: D 85 VAL cc_start: 0.8674 (t) cc_final: 0.8439 (p) REVERT: D 92 MET cc_start: 0.8467 (mmm) cc_final: 0.7964 (mmm) REVERT: D 100 TYR cc_start: 0.7223 (t80) cc_final: 0.6798 (t80) REVERT: D 144 ASP cc_start: 0.8141 (m-30) cc_final: 0.7781 (m-30) REVERT: D 161 TYR cc_start: 0.7977 (t80) cc_final: 0.7742 (t80) REVERT: D 163 GLN cc_start: 0.7264 (tp-100) cc_final: 0.6967 (tp40) REVERT: D 187 MET cc_start: 0.8507 (ttp) cc_final: 0.8197 (ttp) REVERT: D 237 ARG cc_start: 0.7459 (mtp85) cc_final: 0.7256 (mtp85) REVERT: D 243 GLU cc_start: 0.6917 (tt0) cc_final: 0.6580 (tt0) REVERT: D 255 ARG cc_start: 0.7727 (mmt90) cc_final: 0.7481 (mmt-90) REVERT: D 403 ASP cc_start: 0.7445 (m-30) cc_final: 0.7111 (m-30) REVERT: D 443 MET cc_start: 0.7871 (ttp) cc_final: 0.7662 (ttp) REVERT: D 444 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8270 (p) REVERT: D 492 ASP cc_start: 0.7639 (t0) cc_final: 0.7231 (t0) REVERT: D 518 TRP cc_start: 0.8607 (m100) cc_final: 0.8097 (m100) REVERT: D 599 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.5402 (ptt-90) REVERT: D 603 MET cc_start: 0.6930 (mmt) cc_final: 0.6314 (mmt) REVERT: D 625 GLN cc_start: 0.7197 (pt0) cc_final: 0.6988 (pt0) REVERT: D 634 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8528 (mm-40) REVERT: D 648 ASP cc_start: 0.7932 (t0) cc_final: 0.7731 (t0) REVERT: D 655 MET cc_start: 0.7801 (ttt) cc_final: 0.7586 (ttm) REVERT: D 677 LYS cc_start: 0.8393 (mtpt) cc_final: 0.7962 (mtpt) REVERT: D 693 GLN cc_start: 0.6989 (tp40) cc_final: 0.6612 (tp40) REVERT: D 699 ARG cc_start: 0.6878 (ptp-110) cc_final: 0.6619 (ptp-170) REVERT: D 708 TRP cc_start: 0.8293 (p-90) cc_final: 0.8005 (p-90) REVERT: D 709 SER cc_start: 0.8412 (t) cc_final: 0.7837 (p) REVERT: D 739 HIS cc_start: 0.6810 (t70) cc_final: 0.6488 (t-90) REVERT: D 749 ILE cc_start: 0.7358 (mt) cc_final: 0.6833 (tp) REVERT: D 756 TRP cc_start: 0.7968 (m-90) cc_final: 0.7279 (m-90) REVERT: D 799 THR cc_start: 0.8809 (m) cc_final: 0.8316 (p) REVERT: D 924 ASP cc_start: 0.8278 (m-30) cc_final: 0.7898 (t0) REVERT: D 925 MET cc_start: 0.8097 (mmm) cc_final: 0.7890 (mmt) REVERT: D 997 ASP cc_start: 0.7401 (m-30) cc_final: 0.7201 (m-30) REVERT: D 1007 PHE cc_start: 0.8337 (m-10) cc_final: 0.7939 (m-80) REVERT: D 1019 VAL cc_start: 0.8486 (t) cc_final: 0.8058 (p) outliers start: 85 outliers final: 45 residues processed: 912 average time/residue: 0.2140 time to fit residues: 309.1298 Evaluate side-chains 862 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 808 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 977 HIS Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 959 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 100 optimal weight: 0.0020 chunk 377 optimal weight: 3.9990 chunk 362 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 268 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 301 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 890 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN B 890 GLN B1017 GLN C 155 ASN C 540 HIS ** C 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN D 357 HIS D 840 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.118350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099852 restraints weight = 57444.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103301 restraints weight = 26869.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105552 restraints weight = 15392.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.107062 restraints weight = 10307.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108085 restraints weight = 7764.471| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 33792 Z= 0.103 Angle : 0.603 8.145 46104 Z= 0.310 Chirality : 0.044 0.194 4820 Planarity : 0.004 0.042 6088 Dihedral : 5.005 39.085 4478 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.43 % Allowed : 12.33 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.12), residues: 4080 helix: -2.76 (0.24), residues: 356 sheet: -0.09 (0.14), residues: 1380 loop : -2.41 (0.11), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 43 TYR 0.020 0.001 TYR C1016 PHE 0.012 0.001 PHE D 955 TRP 0.018 0.001 TRP C 73 HIS 0.008 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00222 (33792) covalent geometry : angle 0.60336 (46104) hydrogen bonds : bond 0.03397 ( 856) hydrogen bonds : angle 5.61511 ( 2448) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 831 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TRP cc_start: 0.7942 (t60) cc_final: 0.7441 (t60) REVERT: A 67 GLU cc_start: 0.7600 (mp0) cc_final: 0.7346 (mp0) REVERT: A 75 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7260 (tm-30) REVERT: A 84 VAL cc_start: 0.8074 (t) cc_final: 0.7531 (p) REVERT: A 85 VAL cc_start: 0.8687 (t) cc_final: 0.8424 (p) REVERT: A 92 MET cc_start: 0.8244 (mmm) cc_final: 0.7795 (mmm) REVERT: A 144 ASP cc_start: 0.7945 (m-30) cc_final: 0.7297 (m-30) REVERT: A 187 MET cc_start: 0.8310 (ttp) cc_final: 0.8030 (ttp) REVERT: A 211 ASP cc_start: 0.7761 (t0) cc_final: 0.7390 (m-30) REVERT: A 237 ARG cc_start: 0.7138 (mtp85) cc_final: 0.6294 (mtp85) REVERT: A 243 GLU cc_start: 0.7025 (tt0) cc_final: 0.6788 (tt0) REVERT: A 338 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7105 (tm-30) REVERT: A 403 ASP cc_start: 0.7269 (m-30) cc_final: 0.6887 (m-30) REVERT: A 412 GLU cc_start: 0.7176 (tt0) cc_final: 0.6855 (tt0) REVERT: A 492 ASP cc_start: 0.7714 (t0) cc_final: 0.7139 (t0) REVERT: A 553 TRP cc_start: 0.8209 (m100) cc_final: 0.7961 (m100) REVERT: A 585 TRP cc_start: 0.8746 (p-90) cc_final: 0.8082 (p-90) REVERT: A 599 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.6412 (pmt-80) REVERT: A 601 PHE cc_start: 0.8260 (m-80) cc_final: 0.8011 (m-80) REVERT: A 625 GLN cc_start: 0.7130 (pt0) cc_final: 0.6817 (pt0) REVERT: A 634 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8393 (mm-40) REVERT: A 637 GLU cc_start: 0.7074 (tt0) cc_final: 0.6528 (tt0) REVERT: A 655 MET cc_start: 0.7825 (ttt) cc_final: 0.7572 (ttm) REVERT: A 677 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7632 (mtpt) REVERT: A 693 GLN cc_start: 0.6767 (tp40) cc_final: 0.6266 (tm-30) REVERT: A 699 ARG cc_start: 0.6852 (ptp90) cc_final: 0.6585 (ptp-170) REVERT: A 709 SER cc_start: 0.8222 (t) cc_final: 0.7679 (p) REVERT: A 756 TRP cc_start: 0.7558 (m-90) cc_final: 0.7267 (m-90) REVERT: A 792 ASP cc_start: 0.7851 (p0) cc_final: 0.7563 (p0) REVERT: A 842 TRP cc_start: 0.6657 (m-90) cc_final: 0.6168 (m-10) REVERT: A 853 ARG cc_start: 0.7344 (mtt90) cc_final: 0.7124 (mtt90) REVERT: A 924 ASP cc_start: 0.8225 (m-30) cc_final: 0.7734 (t0) REVERT: A 935 ASN cc_start: 0.8818 (p0) cc_final: 0.8583 (p0) REVERT: A 973 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7895 (ptm160) REVERT: A 974 HIS cc_start: 0.7668 (p-80) cc_final: 0.7237 (p-80) REVERT: A 975 LEU cc_start: 0.8596 (mt) cc_final: 0.8104 (mt) REVERT: A 1016 TYR cc_start: 0.7242 (p90) cc_final: 0.6651 (p90) REVERT: B 9 VAL cc_start: 0.9144 (m) cc_final: 0.8890 (p) REVERT: B 62 TRP cc_start: 0.7936 (t60) cc_final: 0.7505 (t60) REVERT: B 67 GLU cc_start: 0.7605 (mp0) cc_final: 0.7353 (mp0) REVERT: B 84 VAL cc_start: 0.8220 (t) cc_final: 0.7671 (p) REVERT: B 85 VAL cc_start: 0.8676 (t) cc_final: 0.8405 (p) REVERT: B 92 MET cc_start: 0.8470 (mmm) cc_final: 0.8006 (mmm) REVERT: B 100 TYR cc_start: 0.6832 (t80) cc_final: 0.6273 (t80) REVERT: B 144 ASP cc_start: 0.8146 (m-30) cc_final: 0.7576 (m-30) REVERT: B 211 ASP cc_start: 0.7571 (t0) cc_final: 0.7290 (t0) REVERT: B 237 ARG cc_start: 0.7316 (mtp85) cc_final: 0.6503 (mtp85) REVERT: B 288 ARG cc_start: 0.7925 (mtt-85) cc_final: 0.7604 (mtt-85) REVERT: B 338 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7320 (tm-30) REVERT: B 403 ASP cc_start: 0.7290 (m-30) cc_final: 0.6849 (m-30) REVERT: B 411 ASP cc_start: 0.7310 (t0) cc_final: 0.6928 (m-30) REVERT: B 492 ASP cc_start: 0.7716 (t0) cc_final: 0.7138 (t0) REVERT: B 544 ASN cc_start: 0.8499 (m-40) cc_final: 0.8271 (m-40) REVERT: B 570 TRP cc_start: 0.7578 (t-100) cc_final: 0.7063 (t-100) REVERT: B 585 TRP cc_start: 0.8642 (p-90) cc_final: 0.7691 (p-90) REVERT: B 599 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.6317 (pmt-80) REVERT: B 634 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8462 (mm-40) REVERT: B 637 GLU cc_start: 0.7157 (tt0) cc_final: 0.6767 (tt0) REVERT: B 655 MET cc_start: 0.7779 (ttt) cc_final: 0.7521 (ttm) REVERT: B 677 LYS cc_start: 0.8395 (mtpt) cc_final: 0.7884 (mtpp) REVERT: B 693 GLN cc_start: 0.6979 (tp40) cc_final: 0.5755 (tp40) REVERT: B 708 TRP cc_start: 0.8259 (p-90) cc_final: 0.7922 (p-90) REVERT: B 709 SER cc_start: 0.8098 (t) cc_final: 0.7571 (p) REVERT: B 720 TRP cc_start: 0.7586 (m-90) cc_final: 0.7191 (m-90) REVERT: B 721 ARG cc_start: 0.7307 (mtp180) cc_final: 0.7086 (mtp-110) REVERT: B 749 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7185 (tp) REVERT: B 761 GLN cc_start: 0.7443 (mp10) cc_final: 0.6947 (mp10) REVERT: B 898 LEU cc_start: 0.6460 (tp) cc_final: 0.6157 (tp) REVERT: B 906 TYR cc_start: 0.7284 (m-10) cc_final: 0.6910 (m-10) REVERT: B 919 ASP cc_start: 0.7915 (m-30) cc_final: 0.7649 (t0) REVERT: B 955 PHE cc_start: 0.8232 (p90) cc_final: 0.8029 (p90) REVERT: B 997 ASP cc_start: 0.7496 (m-30) cc_final: 0.7280 (t0) REVERT: C 9 VAL cc_start: 0.9170 (m) cc_final: 0.8925 (p) REVERT: C 15 ASP cc_start: 0.8080 (m-30) cc_final: 0.7594 (t0) REVERT: C 44 THR cc_start: 0.9031 (t) cc_final: 0.8631 (p) REVERT: C 62 TRP cc_start: 0.8075 (t60) cc_final: 0.7755 (t60) REVERT: C 84 VAL cc_start: 0.8228 (t) cc_final: 0.7701 (p) REVERT: C 85 VAL cc_start: 0.8792 (t) cc_final: 0.8493 (p) REVERT: C 92 MET cc_start: 0.8313 (mmm) cc_final: 0.7832 (mmm) REVERT: C 144 ASP cc_start: 0.8083 (m-30) cc_final: 0.7487 (m-30) REVERT: C 187 MET cc_start: 0.8349 (ttp) cc_final: 0.8029 (ttp) REVERT: C 211 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: C 221 GLN cc_start: 0.8261 (pm20) cc_final: 0.7667 (pm20) REVERT: C 237 ARG cc_start: 0.7456 (ttm-80) cc_final: 0.7182 (mtp85) REVERT: C 289 VAL cc_start: 0.6593 (OUTLIER) cc_final: 0.6227 (m) REVERT: C 349 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7476 (tp) REVERT: C 403 ASP cc_start: 0.7198 (m-30) cc_final: 0.6638 (m-30) REVERT: C 492 ASP cc_start: 0.7686 (t0) cc_final: 0.7251 (t0) REVERT: C 515 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7805 (m) REVERT: C 518 TRP cc_start: 0.8415 (m100) cc_final: 0.7973 (m100) REVERT: C 585 TRP cc_start: 0.8670 (p-90) cc_final: 0.8130 (p-90) REVERT: C 599 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.6120 (pmt-80) REVERT: C 634 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8385 (mm-40) REVERT: C 637 GLU cc_start: 0.6972 (tt0) cc_final: 0.6473 (tt0) REVERT: C 677 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7635 (mtpt) REVERT: C 693 GLN cc_start: 0.7032 (tp40) cc_final: 0.6500 (tp40) REVERT: C 790 ASP cc_start: 0.7292 (m-30) cc_final: 0.7078 (m-30) REVERT: C 792 ASP cc_start: 0.7951 (p0) cc_final: 0.7647 (p0) REVERT: C 808 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7524 (mm-30) REVERT: C 924 ASP cc_start: 0.8267 (m-30) cc_final: 0.8019 (t0) REVERT: C 955 PHE cc_start: 0.8351 (p90) cc_final: 0.7911 (p90) REVERT: C 997 ASP cc_start: 0.7227 (m-30) cc_final: 0.6878 (t70) REVERT: D 62 TRP cc_start: 0.7936 (t60) cc_final: 0.7567 (t60) REVERT: D 67 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7358 (mp0) REVERT: D 75 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7456 (tm-30) REVERT: D 84 VAL cc_start: 0.8170 (t) cc_final: 0.7589 (p) REVERT: D 85 VAL cc_start: 0.8696 (t) cc_final: 0.8456 (p) REVERT: D 92 MET cc_start: 0.8384 (mmm) cc_final: 0.8032 (mmt) REVERT: D 100 TYR cc_start: 0.7130 (t80) cc_final: 0.6543 (t80) REVERT: D 144 ASP cc_start: 0.8143 (m-30) cc_final: 0.7471 (m-30) REVERT: D 163 GLN cc_start: 0.7318 (tp-100) cc_final: 0.7018 (tp40) REVERT: D 187 MET cc_start: 0.8476 (ttp) cc_final: 0.8140 (ttp) REVERT: D 243 GLU cc_start: 0.6895 (tt0) cc_final: 0.6555 (tt0) REVERT: D 288 ARG cc_start: 0.7984 (mtt-85) cc_final: 0.7626 (mtt-85) REVERT: D 403 ASP cc_start: 0.7430 (m-30) cc_final: 0.6942 (m-30) REVERT: D 444 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8256 (t) REVERT: D 492 ASP cc_start: 0.7580 (t0) cc_final: 0.7071 (t0) REVERT: D 518 TRP cc_start: 0.8557 (m100) cc_final: 0.7826 (m100) REVERT: D 585 TRP cc_start: 0.8523 (p-90) cc_final: 0.7739 (p-90) REVERT: D 599 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.6297 (pmt-80) REVERT: D 603 MET cc_start: 0.6376 (mmt) cc_final: 0.6169 (mmt) REVERT: D 634 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8484 (mm-40) REVERT: D 648 ASP cc_start: 0.7949 (t0) cc_final: 0.7685 (t0) REVERT: D 655 MET cc_start: 0.7768 (ttt) cc_final: 0.7560 (ttm) REVERT: D 677 LYS cc_start: 0.8414 (mtpt) cc_final: 0.7703 (mtpt) REVERT: D 693 GLN cc_start: 0.6967 (tp40) cc_final: 0.6594 (tp40) REVERT: D 699 ARG cc_start: 0.6869 (ptp-110) cc_final: 0.6596 (ptp-170) REVERT: D 709 SER cc_start: 0.8253 (t) cc_final: 0.7732 (p) REVERT: D 744 GLU cc_start: 0.8163 (pm20) cc_final: 0.7663 (pm20) REVERT: D 756 TRP cc_start: 0.7923 (m-90) cc_final: 0.7432 (m-90) REVERT: D 853 ARG cc_start: 0.7833 (mtt90) cc_final: 0.7552 (mtt90) REVERT: D 924 ASP cc_start: 0.8195 (m-30) cc_final: 0.7904 (t0) REVERT: D 952 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.7288 (ttm110) REVERT: D 997 ASP cc_start: 0.7481 (m-30) cc_final: 0.7240 (m-30) outliers start: 85 outliers final: 50 residues processed: 875 average time/residue: 0.2236 time to fit residues: 309.8130 Evaluate side-chains 853 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 792 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 977 HIS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 984 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 199 optimal weight: 10.0000 chunk 227 optimal weight: 0.7980 chunk 298 optimal weight: 7.9990 chunk 349 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 352 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 232 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 287 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 155 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 HIS ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN B 226 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 840 HIS ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 840 HIS C 890 GLN ** C 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 ASN D 840 HIS ** D 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.114733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.096596 restraints weight = 57445.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099950 restraints weight = 26919.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102159 restraints weight = 15483.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.103607 restraints weight = 10387.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104515 restraints weight = 7881.654| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33792 Z= 0.190 Angle : 0.670 9.579 46104 Z= 0.350 Chirality : 0.047 0.196 4820 Planarity : 0.005 0.041 6088 Dihedral : 5.114 36.473 4477 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.40 % Allowed : 13.96 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.28 (0.12), residues: 4080 helix: -2.47 (0.25), residues: 364 sheet: -0.02 (0.14), residues: 1408 loop : -2.44 (0.11), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 721 TYR 0.026 0.002 TYR D1016 PHE 0.015 0.002 PHE C 549 TRP 0.020 0.002 TRP B1020 HIS 0.010 0.001 HIS C 974 Details of bonding type rmsd covalent geometry : bond 0.00444 (33792) covalent geometry : angle 0.66955 (46104) hydrogen bonds : bond 0.04848 ( 856) hydrogen bonds : angle 5.52510 ( 2448) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 815 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TRP cc_start: 0.8192 (t60) cc_final: 0.7622 (t60) REVERT: A 67 GLU cc_start: 0.7690 (mp0) cc_final: 0.7472 (mp0) REVERT: A 75 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7235 (tm-30) REVERT: A 84 VAL cc_start: 0.8152 (t) cc_final: 0.7607 (p) REVERT: A 85 VAL cc_start: 0.8736 (t) cc_final: 0.8475 (p) REVERT: A 92 MET cc_start: 0.8297 (mmm) cc_final: 0.7816 (mmm) REVERT: A 100 TYR cc_start: 0.7057 (t80) cc_final: 0.6256 (t80) REVERT: A 131 GLU cc_start: 0.7507 (tp30) cc_final: 0.6913 (tp30) REVERT: A 136 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7999 (mp0) REVERT: A 144 ASP cc_start: 0.7985 (m-30) cc_final: 0.7521 (t0) REVERT: A 187 MET cc_start: 0.8309 (ttp) cc_final: 0.8041 (ttp) REVERT: A 243 GLU cc_start: 0.7110 (tt0) cc_final: 0.6771 (tt0) REVERT: A 338 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7066 (tm-30) REVERT: A 412 GLU cc_start: 0.7346 (tt0) cc_final: 0.7026 (tt0) REVERT: A 492 ASP cc_start: 0.7924 (t0) cc_final: 0.7411 (t0) REVERT: A 585 TRP cc_start: 0.8771 (p-90) cc_final: 0.7708 (p-90) REVERT: A 599 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6686 (pmt-80) REVERT: A 634 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8451 (mm-40) REVERT: A 637 GLU cc_start: 0.7131 (tt0) cc_final: 0.6488 (tt0) REVERT: A 655 MET cc_start: 0.7869 (ttt) cc_final: 0.7587 (ttm) REVERT: A 677 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7630 (mtpt) REVERT: A 693 GLN cc_start: 0.7110 (tp40) cc_final: 0.6475 (tm-30) REVERT: A 748 CYS cc_start: 0.8308 (m) cc_final: 0.8082 (m) REVERT: A 792 ASP cc_start: 0.7788 (p0) cc_final: 0.7521 (p0) REVERT: A 935 ASN cc_start: 0.8883 (p0) cc_final: 0.8591 (p0) REVERT: A 955 PHE cc_start: 0.8404 (p90) cc_final: 0.8169 (p90) REVERT: A 973 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7823 (ptm160) REVERT: A 974 HIS cc_start: 0.7686 (p-80) cc_final: 0.7245 (p-80) REVERT: A 975 LEU cc_start: 0.8657 (mt) cc_final: 0.8139 (mt) REVERT: A 1019 VAL cc_start: 0.8472 (t) cc_final: 0.7989 (p) REVERT: B 9 VAL cc_start: 0.9152 (m) cc_final: 0.8913 (p) REVERT: B 62 TRP cc_start: 0.8160 (t60) cc_final: 0.7472 (t60) REVERT: B 67 GLU cc_start: 0.7639 (mp0) cc_final: 0.7415 (mp0) REVERT: B 84 VAL cc_start: 0.8299 (t) cc_final: 0.7733 (p) REVERT: B 85 VAL cc_start: 0.8703 (t) cc_final: 0.8434 (p) REVERT: B 92 MET cc_start: 0.8475 (mmm) cc_final: 0.7990 (mmm) REVERT: B 100 TYR cc_start: 0.7224 (t80) cc_final: 0.6476 (t80) REVERT: B 144 ASP cc_start: 0.8170 (m-30) cc_final: 0.7640 (m-30) REVERT: B 161 TYR cc_start: 0.7735 (t80) cc_final: 0.7410 (t80) REVERT: B 211 ASP cc_start: 0.7576 (t0) cc_final: 0.7335 (t0) REVERT: B 237 ARG cc_start: 0.7352 (mtp85) cc_final: 0.6441 (mtp85) REVERT: B 245 GLN cc_start: 0.6922 (tp40) cc_final: 0.6623 (tt0) REVERT: B 288 ARG cc_start: 0.7935 (mtt-85) cc_final: 0.6794 (mtt-85) REVERT: B 338 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7429 (tm-30) REVERT: B 403 ASP cc_start: 0.7214 (m-30) cc_final: 0.6812 (m-30) REVERT: B 411 ASP cc_start: 0.7429 (t0) cc_final: 0.6992 (m-30) REVERT: B 412 GLU cc_start: 0.7224 (tt0) cc_final: 0.6995 (tt0) REVERT: B 492 ASP cc_start: 0.7910 (t0) cc_final: 0.7429 (t0) REVERT: B 544 ASN cc_start: 0.8492 (m-40) cc_final: 0.8161 (m-40) REVERT: B 570 TRP cc_start: 0.7639 (t-100) cc_final: 0.7185 (t-100) REVERT: B 585 TRP cc_start: 0.8586 (p-90) cc_final: 0.7399 (p90) REVERT: B 599 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6463 (pmt-80) REVERT: B 634 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8587 (mm110) REVERT: B 637 GLU cc_start: 0.7257 (tt0) cc_final: 0.6723 (tt0) REVERT: B 655 MET cc_start: 0.7856 (ttt) cc_final: 0.7548 (ttm) REVERT: B 677 LYS cc_start: 0.8449 (mtpt) cc_final: 0.7845 (mtpp) REVERT: B 693 GLN cc_start: 0.7038 (tp40) cc_final: 0.6764 (tp40) REVERT: B 708 TRP cc_start: 0.8246 (p-90) cc_final: 0.7816 (p-90) REVERT: B 768 MET cc_start: 0.5111 (ttm) cc_final: 0.4885 (ttm) REVERT: B 898 LEU cc_start: 0.6526 (tp) cc_final: 0.6205 (tp) REVERT: B 905 ASN cc_start: 0.6998 (p0) cc_final: 0.6623 (p0) REVERT: B 919 ASP cc_start: 0.8000 (m-30) cc_final: 0.7440 (t0) REVERT: B 974 HIS cc_start: 0.7353 (p90) cc_final: 0.7088 (p90) REVERT: B 997 ASP cc_start: 0.7411 (m-30) cc_final: 0.7187 (m-30) REVERT: B 1019 VAL cc_start: 0.8343 (t) cc_final: 0.7837 (p) REVERT: C 9 VAL cc_start: 0.9162 (m) cc_final: 0.8933 (p) REVERT: C 15 ASP cc_start: 0.8128 (m-30) cc_final: 0.7623 (t0) REVERT: C 43 ARG cc_start: 0.8320 (ttp80) cc_final: 0.8044 (mtm-85) REVERT: C 44 THR cc_start: 0.9072 (t) cc_final: 0.8667 (p) REVERT: C 62 TRP cc_start: 0.8310 (t60) cc_final: 0.7744 (t60) REVERT: C 84 VAL cc_start: 0.8354 (t) cc_final: 0.7804 (p) REVERT: C 85 VAL cc_start: 0.8828 (t) cc_final: 0.8522 (p) REVERT: C 92 MET cc_start: 0.8263 (mmm) cc_final: 0.7763 (mmm) REVERT: C 100 TYR cc_start: 0.7452 (t80) cc_final: 0.6380 (t80) REVERT: C 136 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8085 (mp0) REVERT: C 144 ASP cc_start: 0.8100 (m-30) cc_final: 0.7521 (m-30) REVERT: C 187 MET cc_start: 0.8381 (ttp) cc_final: 0.8054 (ttp) REVERT: C 211 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: C 221 GLN cc_start: 0.8302 (pm20) cc_final: 0.7700 (pm20) REVERT: C 233 ASP cc_start: 0.7992 (p0) cc_final: 0.7622 (p0) REVERT: C 237 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7224 (mtp85) REVERT: C 349 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7492 (tp) REVERT: C 403 ASP cc_start: 0.7168 (m-30) cc_final: 0.6702 (m-30) REVERT: C 492 ASP cc_start: 0.7877 (t0) cc_final: 0.7500 (t0) REVERT: C 515 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8090 (m) REVERT: C 585 TRP cc_start: 0.8640 (p-90) cc_final: 0.8233 (p-90) REVERT: C 599 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.6266 (pmt-80) REVERT: C 634 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8473 (mm-40) REVERT: C 637 GLU cc_start: 0.7017 (tt0) cc_final: 0.6383 (tt0) REVERT: C 677 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7639 (mtpt) REVERT: C 682 LEU cc_start: 0.8615 (tp) cc_final: 0.8334 (tp) REVERT: C 708 TRP cc_start: 0.8336 (p-90) cc_final: 0.7901 (p-90) REVERT: C 721 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7355 (tpp80) REVERT: C 773 LYS cc_start: 0.7160 (tmmt) cc_final: 0.6938 (tmmt) REVERT: C 792 ASP cc_start: 0.7893 (p0) cc_final: 0.7634 (p0) REVERT: C 808 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7543 (mm-30) REVERT: C 924 ASP cc_start: 0.8330 (m-30) cc_final: 0.8075 (t0) REVERT: C 955 PHE cc_start: 0.8464 (p90) cc_final: 0.8076 (p90) REVERT: C 997 ASP cc_start: 0.7174 (m-30) cc_final: 0.6794 (t0) REVERT: D 62 TRP cc_start: 0.8230 (t60) cc_final: 0.7694 (t60) REVERT: D 67 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7429 (mp0) REVERT: D 75 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7389 (tm-30) REVERT: D 84 VAL cc_start: 0.8253 (t) cc_final: 0.7737 (p) REVERT: D 85 VAL cc_start: 0.8722 (t) cc_final: 0.8507 (p) REVERT: D 92 MET cc_start: 0.8324 (mmm) cc_final: 0.7981 (mmt) REVERT: D 100 TYR cc_start: 0.7318 (t80) cc_final: 0.6661 (t80) REVERT: D 136 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7878 (mp0) REVERT: D 144 ASP cc_start: 0.8142 (m-30) cc_final: 0.7537 (m-30) REVERT: D 187 MET cc_start: 0.8497 (ttp) cc_final: 0.8208 (ttp) REVERT: D 211 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: D 243 GLU cc_start: 0.6918 (tt0) cc_final: 0.6578 (tt0) REVERT: D 403 ASP cc_start: 0.7401 (m-30) cc_final: 0.7152 (m-30) REVERT: D 487 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7718 (tm-30) REVERT: D 492 ASP cc_start: 0.7847 (t0) cc_final: 0.7435 (t0) REVERT: D 515 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7919 (m) REVERT: D 599 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6586 (pmt-80) REVERT: D 603 MET cc_start: 0.6836 (mmt) cc_final: 0.6189 (mmt) REVERT: D 634 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8530 (mm-40) REVERT: D 655 MET cc_start: 0.7861 (ttt) cc_final: 0.7631 (ttm) REVERT: D 677 LYS cc_start: 0.8460 (mtpt) cc_final: 0.7942 (mtpt) REVERT: D 693 GLN cc_start: 0.6962 (tp40) cc_final: 0.6591 (tp40) REVERT: D 699 ARG cc_start: 0.6931 (ptp-110) cc_final: 0.6684 (ptp-170) REVERT: D 709 SER cc_start: 0.8177 (t) cc_final: 0.7677 (p) REVERT: D 773 LYS cc_start: 0.7591 (tmtt) cc_final: 0.7020 (tmtt) REVERT: D 906 TYR cc_start: 0.7245 (m-10) cc_final: 0.7040 (m-10) REVERT: D 924 ASP cc_start: 0.8224 (m-30) cc_final: 0.7958 (t0) REVERT: D 952 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7325 (ttm110) REVERT: D 1019 VAL cc_start: 0.8580 (t) cc_final: 0.8094 (p) outliers start: 119 outliers final: 76 residues processed: 877 average time/residue: 0.2181 time to fit residues: 302.5899 Evaluate side-chains 872 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 786 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 977 HIS Chi-restraints excluded: chain A residue 1017 GLN Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 772 ASP Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 977 HIS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1018 LEU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 984 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 334 optimal weight: 5.9990 chunk 105 optimal weight: 0.0040 chunk 371 optimal weight: 8.9990 chunk 375 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 297 optimal weight: 7.9990 chunk 257 optimal weight: 4.9990 chunk 6 optimal weight: 0.0020 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 HIS ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 HIS ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 840 HIS ** C 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 840 HIS ** D 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097248 restraints weight = 57518.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.100624 restraints weight = 26909.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.102852 restraints weight = 15441.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104301 restraints weight = 10329.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105267 restraints weight = 7799.265| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33792 Z= 0.153 Angle : 0.640 8.301 46104 Z= 0.332 Chirality : 0.046 0.245 4820 Planarity : 0.004 0.041 6088 Dihedral : 4.998 38.769 4477 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.49 % Allowed : 14.99 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.13), residues: 4080 helix: -2.02 (0.28), residues: 340 sheet: 0.05 (0.14), residues: 1408 loop : -2.39 (0.11), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 721 TYR 0.023 0.002 TYR D1016 PHE 0.012 0.001 PHE C 549 TRP 0.029 0.002 TRP A 842 HIS 0.016 0.001 HIS C 974 Details of bonding type rmsd covalent geometry : bond 0.00354 (33792) covalent geometry : angle 0.63957 (46104) hydrogen bonds : bond 0.04209 ( 856) hydrogen bonds : angle 5.32551 ( 2448) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 818 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TRP cc_start: 0.8163 (t60) cc_final: 0.7598 (t60) REVERT: A 67 GLU cc_start: 0.7738 (mp0) cc_final: 0.7517 (mp0) REVERT: A 75 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7226 (tm-30) REVERT: A 84 VAL cc_start: 0.8195 (t) cc_final: 0.7634 (p) REVERT: A 85 VAL cc_start: 0.8747 (t) cc_final: 0.8485 (p) REVERT: A 92 MET cc_start: 0.8301 (mmm) cc_final: 0.7811 (mmm) REVERT: A 131 GLU cc_start: 0.7554 (tp30) cc_final: 0.6950 (tp30) REVERT: A 144 ASP cc_start: 0.7972 (m-30) cc_final: 0.7498 (t0) REVERT: A 187 MET cc_start: 0.8274 (ttp) cc_final: 0.8043 (ttp) REVERT: A 221 GLN cc_start: 0.8148 (pm20) cc_final: 0.7900 (pm20) REVERT: A 243 GLU cc_start: 0.7033 (tt0) cc_final: 0.6749 (tt0) REVERT: A 338 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7204 (tm-30) REVERT: A 403 ASP cc_start: 0.7839 (t0) cc_final: 0.7257 (m-30) REVERT: A 412 GLU cc_start: 0.7311 (tt0) cc_final: 0.7038 (tt0) REVERT: A 473 ARG cc_start: 0.8047 (mmm160) cc_final: 0.7797 (tpt170) REVERT: A 492 ASP cc_start: 0.7907 (t0) cc_final: 0.7436 (t0) REVERT: A 585 TRP cc_start: 0.8795 (p-90) cc_final: 0.7624 (p-90) REVERT: A 599 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6618 (pmt-80) REVERT: A 634 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8451 (mm-40) REVERT: A 637 GLU cc_start: 0.7142 (tt0) cc_final: 0.6427 (tt0) REVERT: A 655 MET cc_start: 0.7859 (ttt) cc_final: 0.7589 (ttm) REVERT: A 677 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7534 (mtpp) REVERT: A 693 GLN cc_start: 0.7011 (tp40) cc_final: 0.6659 (tm-30) REVERT: A 739 HIS cc_start: 0.7367 (t-90) cc_final: 0.7024 (t-90) REVERT: A 748 CYS cc_start: 0.8290 (m) cc_final: 0.8040 (m) REVERT: A 756 TRP cc_start: 0.7520 (m-90) cc_final: 0.7002 (m-90) REVERT: A 784 PHE cc_start: 0.7858 (m-10) cc_final: 0.7654 (m-10) REVERT: A 792 ASP cc_start: 0.7750 (p0) cc_final: 0.7488 (p0) REVERT: A 935 ASN cc_start: 0.8889 (p0) cc_final: 0.8625 (p0) REVERT: A 945 ASN cc_start: 0.7510 (m-40) cc_final: 0.7188 (t0) REVERT: A 955 PHE cc_start: 0.8399 (p90) cc_final: 0.8174 (p90) REVERT: A 973 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7757 (ptm160) REVERT: A 974 HIS cc_start: 0.7672 (p-80) cc_final: 0.7203 (p-80) REVERT: A 975 LEU cc_start: 0.8645 (mt) cc_final: 0.8128 (mt) REVERT: A 997 ASP cc_start: 0.7119 (t0) cc_final: 0.6859 (t0) REVERT: A 1019 VAL cc_start: 0.8475 (t) cc_final: 0.7994 (p) REVERT: B 9 VAL cc_start: 0.9134 (m) cc_final: 0.8907 (p) REVERT: B 62 TRP cc_start: 0.8099 (t60) cc_final: 0.7466 (t60) REVERT: B 67 GLU cc_start: 0.7621 (mp0) cc_final: 0.7373 (mp0) REVERT: B 84 VAL cc_start: 0.8270 (t) cc_final: 0.7708 (p) REVERT: B 85 VAL cc_start: 0.8701 (t) cc_final: 0.8438 (p) REVERT: B 92 MET cc_start: 0.8453 (mmm) cc_final: 0.7963 (mmm) REVERT: B 100 TYR cc_start: 0.7198 (t80) cc_final: 0.6359 (t80) REVERT: B 136 GLU cc_start: 0.8319 (mp0) cc_final: 0.7934 (mp0) REVERT: B 144 ASP cc_start: 0.8151 (m-30) cc_final: 0.7608 (m-30) REVERT: B 211 ASP cc_start: 0.7568 (t0) cc_final: 0.7234 (t0) REVERT: B 237 ARG cc_start: 0.7324 (mtp85) cc_final: 0.6438 (mtp85) REVERT: B 288 ARG cc_start: 0.7922 (mtt-85) cc_final: 0.7310 (mtt-85) REVERT: B 299 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7705 (mttp) REVERT: B 338 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7424 (tm-30) REVERT: B 403 ASP cc_start: 0.7244 (m-30) cc_final: 0.6862 (m-30) REVERT: B 411 ASP cc_start: 0.7347 (t0) cc_final: 0.6913 (m-30) REVERT: B 412 GLU cc_start: 0.7162 (tt0) cc_final: 0.6867 (tt0) REVERT: B 492 ASP cc_start: 0.7916 (t0) cc_final: 0.7447 (t0) REVERT: B 544 ASN cc_start: 0.8492 (m-40) cc_final: 0.8167 (m-40) REVERT: B 585 TRP cc_start: 0.8558 (p-90) cc_final: 0.7778 (p-90) REVERT: B 599 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.6404 (pmt-80) REVERT: B 634 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8608 (mm110) REVERT: B 637 GLU cc_start: 0.7191 (tt0) cc_final: 0.6500 (tt0) REVERT: B 655 MET cc_start: 0.7844 (ttt) cc_final: 0.7531 (ttm) REVERT: B 677 LYS cc_start: 0.8468 (mtpt) cc_final: 0.7835 (mtpt) REVERT: B 693 GLN cc_start: 0.7046 (tp40) cc_final: 0.6779 (tp40) REVERT: B 708 TRP cc_start: 0.8252 (p-90) cc_final: 0.7792 (p-90) REVERT: B 768 MET cc_start: 0.5037 (ttm) cc_final: 0.4461 (ttm) REVERT: B 898 LEU cc_start: 0.6461 (tp) cc_final: 0.6157 (tp) REVERT: B 905 ASN cc_start: 0.7024 (p0) cc_final: 0.6679 (p0) REVERT: B 908 ASP cc_start: 0.7837 (t0) cc_final: 0.7429 (t0) REVERT: B 919 ASP cc_start: 0.8030 (m-30) cc_final: 0.7417 (t0) REVERT: B 955 PHE cc_start: 0.8296 (p90) cc_final: 0.8051 (p90) REVERT: C 9 VAL cc_start: 0.9151 (m) cc_final: 0.8940 (p) REVERT: C 15 ASP cc_start: 0.8264 (m-30) cc_final: 0.7827 (t0) REVERT: C 43 ARG cc_start: 0.8295 (ttp80) cc_final: 0.8022 (mtm-85) REVERT: C 44 THR cc_start: 0.9011 (t) cc_final: 0.7893 (p) REVERT: C 45 ASP cc_start: 0.8538 (t70) cc_final: 0.8178 (t0) REVERT: C 46 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.8001 (ttm110) REVERT: C 62 TRP cc_start: 0.8242 (t60) cc_final: 0.7767 (t60) REVERT: C 84 VAL cc_start: 0.8276 (t) cc_final: 0.7767 (p) REVERT: C 85 VAL cc_start: 0.8795 (t) cc_final: 0.8496 (p) REVERT: C 92 MET cc_start: 0.8257 (mmm) cc_final: 0.7745 (mmm) REVERT: C 144 ASP cc_start: 0.8028 (m-30) cc_final: 0.7199 (m-30) REVERT: C 187 MET cc_start: 0.8337 (ttp) cc_final: 0.8036 (ttp) REVERT: C 211 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: C 221 GLN cc_start: 0.8293 (pm20) cc_final: 0.7753 (pm20) REVERT: C 237 ARG cc_start: 0.7414 (ttm-80) cc_final: 0.7115 (mtp85) REVERT: C 245 GLN cc_start: 0.6795 (tp40) cc_final: 0.6465 (tp40) REVERT: C 349 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7467 (tp) REVERT: C 403 ASP cc_start: 0.7189 (m-30) cc_final: 0.6647 (m-30) REVERT: C 492 ASP cc_start: 0.7865 (t0) cc_final: 0.7507 (t0) REVERT: C 515 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8046 (m) REVERT: C 585 TRP cc_start: 0.8645 (p-90) cc_final: 0.8131 (p-90) REVERT: C 599 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6253 (pmt-80) REVERT: C 634 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8443 (mm-40) REVERT: C 637 GLU cc_start: 0.7093 (tt0) cc_final: 0.6371 (tt0) REVERT: C 677 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7575 (mtpt) REVERT: C 682 LEU cc_start: 0.8567 (tp) cc_final: 0.8303 (tp) REVERT: C 693 GLN cc_start: 0.7189 (tp40) cc_final: 0.6092 (tp40) REVERT: C 721 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.7249 (mtp-110) REVERT: C 792 ASP cc_start: 0.7829 (p0) cc_final: 0.7540 (p0) REVERT: C 808 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7426 (mm-30) REVERT: C 924 ASP cc_start: 0.8332 (m-30) cc_final: 0.8010 (t0) REVERT: C 955 PHE cc_start: 0.8462 (p90) cc_final: 0.7928 (p90) REVERT: C 997 ASP cc_start: 0.7138 (m-30) cc_final: 0.6757 (t0) REVERT: D 15 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7783 (t0) REVERT: D 62 TRP cc_start: 0.8133 (t60) cc_final: 0.7690 (t60) REVERT: D 67 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7424 (mp0) REVERT: D 75 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7355 (tm-30) REVERT: D 84 VAL cc_start: 0.8223 (t) cc_final: 0.7705 (p) REVERT: D 85 VAL cc_start: 0.8707 (t) cc_final: 0.8482 (p) REVERT: D 100 TYR cc_start: 0.7111 (t80) cc_final: 0.6297 (t80) REVERT: D 144 ASP cc_start: 0.8122 (m-30) cc_final: 0.7484 (m-30) REVERT: D 187 MET cc_start: 0.8466 (ttp) cc_final: 0.8198 (ttp) REVERT: D 211 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7366 (m-30) REVERT: D 243 GLU cc_start: 0.6957 (tt0) cc_final: 0.6648 (tt0) REVERT: D 245 GLN cc_start: 0.7204 (tt0) cc_final: 0.6880 (tt0) REVERT: D 288 ARG cc_start: 0.7749 (mtt-85) cc_final: 0.7479 (mtt90) REVERT: D 403 ASP cc_start: 0.7504 (m-30) cc_final: 0.6982 (m-30) REVERT: D 411 ASP cc_start: 0.7252 (t0) cc_final: 0.6809 (m-30) REVERT: D 492 ASP cc_start: 0.7834 (t0) cc_final: 0.7449 (t0) REVERT: D 599 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6480 (pmt-80) REVERT: D 603 MET cc_start: 0.6720 (mmt) cc_final: 0.6283 (mmt) REVERT: D 634 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8548 (mm-40) REVERT: D 655 MET cc_start: 0.7855 (ttt) cc_final: 0.7593 (ttm) REVERT: D 677 LYS cc_start: 0.8397 (mtpt) cc_final: 0.7914 (mtpt) REVERT: D 693 GLN cc_start: 0.7185 (tp40) cc_final: 0.6741 (tp40) REVERT: D 699 ARG cc_start: 0.6801 (ptp-110) cc_final: 0.6564 (ptp-170) REVERT: D 709 SER cc_start: 0.8133 (t) cc_final: 0.7524 (p) REVERT: D 744 GLU cc_start: 0.8221 (pm20) cc_final: 0.7646 (pm20) REVERT: D 749 ILE cc_start: 0.7609 (tp) cc_final: 0.7153 (tp) REVERT: D 756 TRP cc_start: 0.8154 (m-90) cc_final: 0.7853 (m-90) REVERT: D 768 MET cc_start: 0.6184 (ttm) cc_final: 0.5978 (ttm) REVERT: D 773 LYS cc_start: 0.7484 (tmtt) cc_final: 0.7230 (tmtt) REVERT: D 924 ASP cc_start: 0.8251 (m-30) cc_final: 0.7971 (t0) REVERT: D 952 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7262 (ttm110) REVERT: D 1019 VAL cc_start: 0.8578 (t) cc_final: 0.8093 (p) outliers start: 122 outliers final: 84 residues processed: 883 average time/residue: 0.1975 time to fit residues: 276.9085 Evaluate side-chains 895 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 801 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 977 HIS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1017 GLN Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1018 LEU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 871 GLU Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 977 HIS Chi-restraints excluded: chain D residue 984 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 361 optimal weight: 0.8980 chunk 382 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 331 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 325 optimal weight: 3.9990 chunk 210 optimal weight: 0.0670 chunk 300 optimal weight: 5.9990 chunk 263 optimal weight: 1.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 HIS ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 HIS ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 840 HIS ** C 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 840 HIS ** D 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099515 restraints weight = 57107.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.102949 restraints weight = 26776.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.105171 restraints weight = 15337.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106634 restraints weight = 10244.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107628 restraints weight = 7725.599| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 33792 Z= 0.104 Angle : 0.614 8.584 46104 Z= 0.312 Chirality : 0.045 0.188 4820 Planarity : 0.004 0.038 6088 Dihedral : 4.716 39.375 4477 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.86 % Allowed : 16.05 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.13), residues: 4080 helix: -1.84 (0.28), residues: 340 sheet: 0.26 (0.14), residues: 1400 loop : -2.30 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 721 TYR 0.022 0.001 TYR D1016 PHE 0.008 0.001 PHE C 150 TRP 0.038 0.001 TRP C 842 HIS 0.017 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00233 (33792) covalent geometry : angle 0.61372 (46104) hydrogen bonds : bond 0.03271 ( 856) hydrogen bonds : angle 5.03255 ( 2448) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 824 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.7480 (ttm-80) REVERT: A 46 ARG cc_start: 0.8220 (tpp80) cc_final: 0.7605 (ttm110) REVERT: A 62 TRP cc_start: 0.8056 (t60) cc_final: 0.7504 (t60) REVERT: A 67 GLU cc_start: 0.7726 (mp0) cc_final: 0.7502 (mp0) REVERT: A 75 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7194 (tm-30) REVERT: A 84 VAL cc_start: 0.8123 (t) cc_final: 0.7557 (p) REVERT: A 85 VAL cc_start: 0.8726 (t) cc_final: 0.8459 (p) REVERT: A 136 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7804 (mp0) REVERT: A 144 ASP cc_start: 0.7957 (m-30) cc_final: 0.7164 (m-30) REVERT: A 187 MET cc_start: 0.8249 (ttp) cc_final: 0.8008 (ttp) REVERT: A 221 GLN cc_start: 0.8107 (pm20) cc_final: 0.7850 (pm20) REVERT: A 243 GLU cc_start: 0.7031 (tt0) cc_final: 0.6790 (tt0) REVERT: A 338 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7220 (tm-30) REVERT: A 412 GLU cc_start: 0.7212 (tt0) cc_final: 0.6909 (tt0) REVERT: A 473 ARG cc_start: 0.8067 (mmm160) cc_final: 0.7858 (tpt170) REVERT: A 492 ASP cc_start: 0.7822 (t0) cc_final: 0.7315 (t0) REVERT: A 585 TRP cc_start: 0.8783 (p-90) cc_final: 0.7914 (p-90) REVERT: A 599 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6648 (pmt-80) REVERT: A 634 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8400 (mm-40) REVERT: A 637 GLU cc_start: 0.7254 (tt0) cc_final: 0.6528 (tt0) REVERT: A 655 MET cc_start: 0.7845 (ttt) cc_final: 0.7581 (ttm) REVERT: A 677 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7486 (mtpp) REVERT: A 693 GLN cc_start: 0.6969 (tp40) cc_final: 0.6507 (tm-30) REVERT: A 721 ARG cc_start: 0.7801 (tpp80) cc_final: 0.7356 (mtp-110) REVERT: A 726 LEU cc_start: 0.7787 (tt) cc_final: 0.7542 (tp) REVERT: A 744 GLU cc_start: 0.8469 (pm20) cc_final: 0.8267 (pm20) REVERT: A 748 CYS cc_start: 0.8284 (m) cc_final: 0.8036 (m) REVERT: A 756 TRP cc_start: 0.7433 (m-90) cc_final: 0.7004 (m-90) REVERT: A 784 PHE cc_start: 0.7729 (m-10) cc_final: 0.7377 (m-10) REVERT: A 792 ASP cc_start: 0.7753 (p0) cc_final: 0.7481 (p0) REVERT: A 924 ASP cc_start: 0.8167 (m-30) cc_final: 0.7917 (p0) REVERT: A 925 MET cc_start: 0.7855 (mmt) cc_final: 0.6894 (mmt) REVERT: A 935 ASN cc_start: 0.8835 (p0) cc_final: 0.8593 (p0) REVERT: A 945 ASN cc_start: 0.7451 (m-40) cc_final: 0.7125 (t0) REVERT: A 955 PHE cc_start: 0.8324 (p90) cc_final: 0.8091 (p90) REVERT: A 973 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7634 (ptm160) REVERT: A 974 HIS cc_start: 0.7655 (p-80) cc_final: 0.7201 (p-80) REVERT: A 975 LEU cc_start: 0.8619 (mt) cc_final: 0.8159 (mt) REVERT: A 997 ASP cc_start: 0.7176 (t0) cc_final: 0.6842 (t0) REVERT: A 1016 TYR cc_start: 0.7238 (p90) cc_final: 0.6947 (p90) REVERT: B 9 VAL cc_start: 0.9110 (m) cc_final: 0.8885 (p) REVERT: B 26 ARG cc_start: 0.7999 (mtp180) cc_final: 0.7703 (ttp80) REVERT: B 43 ARG cc_start: 0.8348 (mtm110) cc_final: 0.7760 (ttm-80) REVERT: B 62 TRP cc_start: 0.7966 (t60) cc_final: 0.7447 (t60) REVERT: B 67 GLU cc_start: 0.7615 (mp0) cc_final: 0.7369 (mp0) REVERT: B 84 VAL cc_start: 0.8216 (t) cc_final: 0.7647 (p) REVERT: B 85 VAL cc_start: 0.8675 (t) cc_final: 0.8418 (p) REVERT: B 92 MET cc_start: 0.8443 (mmm) cc_final: 0.7975 (mmm) REVERT: B 144 ASP cc_start: 0.8151 (m-30) cc_final: 0.7416 (m-30) REVERT: B 211 ASP cc_start: 0.7527 (t0) cc_final: 0.7240 (t0) REVERT: B 221 GLN cc_start: 0.8301 (pm20) cc_final: 0.7973 (pm20) REVERT: B 245 GLN cc_start: 0.7191 (tt0) cc_final: 0.6624 (tt0) REVERT: B 288 ARG cc_start: 0.7761 (mtt-85) cc_final: 0.7140 (mtt90) REVERT: B 299 LYS cc_start: 0.8102 (mmmm) cc_final: 0.7650 (mttp) REVERT: B 338 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7381 (tm-30) REVERT: B 403 ASP cc_start: 0.7299 (m-30) cc_final: 0.6880 (m-30) REVERT: B 411 ASP cc_start: 0.7284 (t0) cc_final: 0.6934 (m-30) REVERT: B 492 ASP cc_start: 0.7854 (t0) cc_final: 0.7370 (t0) REVERT: B 544 ASN cc_start: 0.8439 (m-40) cc_final: 0.8134 (m-40) REVERT: B 578 TYR cc_start: 0.8686 (m-10) cc_final: 0.8474 (m-10) REVERT: B 585 TRP cc_start: 0.8562 (p-90) cc_final: 0.7834 (p-90) REVERT: B 599 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6208 (pmt-80) REVERT: B 634 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8537 (mm-40) REVERT: B 637 GLU cc_start: 0.7210 (tt0) cc_final: 0.6680 (tt0) REVERT: B 655 MET cc_start: 0.7814 (ttt) cc_final: 0.7497 (ttm) REVERT: B 677 LYS cc_start: 0.8430 (mtpt) cc_final: 0.7807 (mtpt) REVERT: B 693 GLN cc_start: 0.6914 (tp40) cc_final: 0.6707 (tp40) REVERT: B 708 TRP cc_start: 0.8303 (p-90) cc_final: 0.7841 (p-90) REVERT: B 768 MET cc_start: 0.4869 (ttm) cc_final: 0.4238 (ttm) REVERT: B 898 LEU cc_start: 0.6391 (tp) cc_final: 0.6084 (tp) REVERT: B 906 TYR cc_start: 0.7234 (m-10) cc_final: 0.6953 (m-10) REVERT: B 919 ASP cc_start: 0.8046 (m-30) cc_final: 0.7417 (t0) REVERT: B 997 ASP cc_start: 0.7384 (m-30) cc_final: 0.7077 (t0) REVERT: C 14 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7906 (mtp85) REVERT: C 15 ASP cc_start: 0.8082 (m-30) cc_final: 0.7629 (t0) REVERT: C 44 THR cc_start: 0.8978 (t) cc_final: 0.8513 (p) REVERT: C 45 ASP cc_start: 0.8560 (t70) cc_final: 0.8226 (t0) REVERT: C 62 TRP cc_start: 0.8134 (t60) cc_final: 0.7696 (t60) REVERT: C 84 VAL cc_start: 0.8211 (t) cc_final: 0.7695 (p) REVERT: C 85 VAL cc_start: 0.8770 (t) cc_final: 0.8467 (p) REVERT: C 92 MET cc_start: 0.8250 (mmm) cc_final: 0.7729 (mmm) REVERT: C 136 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8076 (mp0) REVERT: C 144 ASP cc_start: 0.8008 (m-30) cc_final: 0.7177 (m-30) REVERT: C 187 MET cc_start: 0.8318 (ttp) cc_final: 0.8017 (ttp) REVERT: C 211 ASP cc_start: 0.7762 (t0) cc_final: 0.7361 (m-30) REVERT: C 221 GLN cc_start: 0.8264 (pm20) cc_final: 0.7703 (pm20) REVERT: C 237 ARG cc_start: 0.7363 (ttm-80) cc_final: 0.6985 (mtp85) REVERT: C 245 GLN cc_start: 0.6722 (tp40) cc_final: 0.6364 (tp40) REVERT: C 349 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7454 (tp) REVERT: C 403 ASP cc_start: 0.7168 (m-30) cc_final: 0.6611 (m-30) REVERT: C 492 ASP cc_start: 0.7791 (t0) cc_final: 0.7404 (t0) REVERT: C 515 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.7951 (m) REVERT: C 542 MET cc_start: 0.8321 (ptt) cc_final: 0.7925 (ptt) REVERT: C 599 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.6184 (pmt-80) REVERT: C 634 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8390 (mm-40) REVERT: C 637 GLU cc_start: 0.7065 (tt0) cc_final: 0.6236 (tt0) REVERT: C 677 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7522 (mtpt) REVERT: C 682 LEU cc_start: 0.8551 (tp) cc_final: 0.8317 (tp) REVERT: C 693 GLN cc_start: 0.7175 (tp40) cc_final: 0.6403 (tp40) REVERT: C 721 ARG cc_start: 0.7648 (ttm-80) cc_final: 0.7193 (mtp-110) REVERT: C 756 TRP cc_start: 0.7500 (m-90) cc_final: 0.7044 (m-90) REVERT: C 792 ASP cc_start: 0.7820 (p0) cc_final: 0.7570 (p0) REVERT: C 808 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7494 (mm-30) REVERT: C 924 ASP cc_start: 0.8164 (m-30) cc_final: 0.7895 (t0) REVERT: C 955 PHE cc_start: 0.8434 (p90) cc_final: 0.8208 (p90) REVERT: C 997 ASP cc_start: 0.7174 (m-30) cc_final: 0.6773 (t0) REVERT: D 62 TRP cc_start: 0.8014 (t60) cc_final: 0.7574 (t60) REVERT: D 67 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7371 (mp0) REVERT: D 75 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7278 (tm-30) REVERT: D 84 VAL cc_start: 0.8152 (t) cc_final: 0.7611 (p) REVERT: D 85 VAL cc_start: 0.8655 (t) cc_final: 0.8416 (p) REVERT: D 100 TYR cc_start: 0.7198 (t80) cc_final: 0.6438 (t80) REVERT: D 131 GLU cc_start: 0.7414 (tp30) cc_final: 0.6982 (tp30) REVERT: D 144 ASP cc_start: 0.8096 (m-30) cc_final: 0.7443 (m-30) REVERT: D 170 GLU cc_start: 0.6797 (pm20) cc_final: 0.6528 (pm20) REVERT: D 187 MET cc_start: 0.8442 (ttp) cc_final: 0.8167 (ttp) REVERT: D 211 ASP cc_start: 0.7733 (t0) cc_final: 0.7309 (m-30) REVERT: D 243 GLU cc_start: 0.6937 (tt0) cc_final: 0.6616 (tt0) REVERT: D 245 GLN cc_start: 0.7147 (tt0) cc_final: 0.6883 (tt0) REVERT: D 288 ARG cc_start: 0.7727 (mtt-85) cc_final: 0.7285 (mtt90) REVERT: D 403 ASP cc_start: 0.7479 (m-30) cc_final: 0.7083 (m-30) REVERT: D 411 ASP cc_start: 0.7179 (t0) cc_final: 0.6763 (m-30) REVERT: D 473 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.7689 (tpt170) REVERT: D 492 ASP cc_start: 0.7766 (t0) cc_final: 0.7341 (t0) REVERT: D 599 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6388 (pmt-80) REVERT: D 634 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8519 (mm-40) REVERT: D 655 MET cc_start: 0.7841 (ttt) cc_final: 0.7586 (ttm) REVERT: D 677 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8119 (mtpt) REVERT: D 693 GLN cc_start: 0.7127 (tp40) cc_final: 0.6789 (tp40) REVERT: D 699 ARG cc_start: 0.6637 (ptp-110) cc_final: 0.6415 (ptp-170) REVERT: D 709 SER cc_start: 0.8056 (t) cc_final: 0.7541 (p) REVERT: D 721 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7212 (ttp80) REVERT: D 744 GLU cc_start: 0.8289 (pm20) cc_final: 0.7824 (pm20) REVERT: D 749 ILE cc_start: 0.7577 (tp) cc_final: 0.7261 (tp) REVERT: D 761 GLN cc_start: 0.6974 (mp10) cc_final: 0.6739 (mp10) REVERT: D 924 ASP cc_start: 0.8246 (m-30) cc_final: 0.7976 (t0) REVERT: D 952 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7257 (ttm110) REVERT: D 961 ARG cc_start: 0.7637 (tpt-90) cc_final: 0.7379 (ttt90) outliers start: 100 outliers final: 69 residues processed: 876 average time/residue: 0.2159 time to fit residues: 297.6029 Evaluate side-chains 880 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 804 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 845 GLN Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 977 HIS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1017 GLN Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1018 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 984 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 162 optimal weight: 0.0370 chunk 98 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 280 optimal weight: 0.0870 chunk 171 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 374 optimal weight: 6.9990 chunk 279 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 HIS ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 ASN B 840 HIS ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 840 HIS C 844 HIS ** C 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 HIS ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 840 HIS ** D 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101043 restraints weight = 57377.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104501 restraints weight = 26891.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106760 restraints weight = 15390.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.108160 restraints weight = 10245.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109239 restraints weight = 7781.822| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 33792 Z= 0.100 Angle : 0.597 7.696 46104 Z= 0.303 Chirality : 0.044 0.272 4820 Planarity : 0.004 0.041 6088 Dihedral : 4.461 38.750 4477 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.69 % Allowed : 16.88 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.13), residues: 4080 helix: -1.57 (0.29), residues: 340 sheet: 0.42 (0.14), residues: 1400 loop : -2.17 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 46 TYR 0.020 0.001 TYR D1016 PHE 0.019 0.001 PHE B 955 TRP 0.026 0.001 TRP A 842 HIS 0.013 0.001 HIS B 974 Details of bonding type rmsd covalent geometry : bond 0.00222 (33792) covalent geometry : angle 0.59653 (46104) hydrogen bonds : bond 0.02957 ( 856) hydrogen bonds : angle 4.80403 ( 2448) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 808 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TRP cc_start: 0.8007 (t60) cc_final: 0.7502 (t60) REVERT: A 67 GLU cc_start: 0.7695 (mp0) cc_final: 0.7480 (mp0) REVERT: A 75 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7102 (tm-30) REVERT: A 84 VAL cc_start: 0.8129 (t) cc_final: 0.7564 (p) REVERT: A 85 VAL cc_start: 0.8712 (t) cc_final: 0.8437 (p) REVERT: A 136 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7851 (mp0) REVERT: A 144 ASP cc_start: 0.7925 (m-30) cc_final: 0.7163 (m-30) REVERT: A 161 TYR cc_start: 0.7885 (t80) cc_final: 0.7644 (t80) REVERT: A 187 MET cc_start: 0.8244 (ttp) cc_final: 0.7999 (ttp) REVERT: A 243 GLU cc_start: 0.7046 (tt0) cc_final: 0.6770 (tt0) REVERT: A 245 GLN cc_start: 0.6708 (tp40) cc_final: 0.6415 (tp40) REVERT: A 255 ARG cc_start: 0.7770 (mpt-90) cc_final: 0.7305 (mmt90) REVERT: A 338 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7156 (tm-30) REVERT: A 412 GLU cc_start: 0.7135 (tt0) cc_final: 0.6848 (tt0) REVERT: A 492 ASP cc_start: 0.7778 (t0) cc_final: 0.7250 (t0) REVERT: A 494 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7999 (p) REVERT: A 585 TRP cc_start: 0.8785 (p-90) cc_final: 0.8057 (p-90) REVERT: A 599 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6636 (pmt-80) REVERT: A 634 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8412 (mm-40) REVERT: A 637 GLU cc_start: 0.7261 (tt0) cc_final: 0.6573 (tt0) REVERT: A 655 MET cc_start: 0.7836 (ttt) cc_final: 0.7572 (ttm) REVERT: A 677 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7518 (mtpp) REVERT: A 693 GLN cc_start: 0.6972 (tp40) cc_final: 0.6475 (tm-30) REVERT: A 708 TRP cc_start: 0.8423 (p-90) cc_final: 0.8018 (p-90) REVERT: A 721 ARG cc_start: 0.7766 (tpp80) cc_final: 0.7438 (mtp-110) REVERT: A 739 HIS cc_start: 0.7326 (t-90) cc_final: 0.6900 (t-90) REVERT: A 749 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7341 (tp) REVERT: A 756 TRP cc_start: 0.7356 (m-90) cc_final: 0.7121 (m-90) REVERT: A 792 ASP cc_start: 0.7754 (p0) cc_final: 0.7494 (p0) REVERT: A 935 ASN cc_start: 0.8925 (p0) cc_final: 0.8653 (p0) REVERT: A 945 ASN cc_start: 0.7375 (m-40) cc_final: 0.7087 (t0) REVERT: A 973 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7579 (ptm160) REVERT: A 974 HIS cc_start: 0.7634 (p-80) cc_final: 0.7170 (p-80) REVERT: A 975 LEU cc_start: 0.8598 (mt) cc_final: 0.8139 (mt) REVERT: A 997 ASP cc_start: 0.7097 (t0) cc_final: 0.6748 (t0) REVERT: A 1016 TYR cc_start: 0.7112 (p90) cc_final: 0.6473 (p90) REVERT: B 26 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7721 (ttp80) REVERT: B 46 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7641 (ttm110) REVERT: B 62 TRP cc_start: 0.7910 (t60) cc_final: 0.7429 (t60) REVERT: B 67 GLU cc_start: 0.7600 (mp0) cc_final: 0.7352 (mp0) REVERT: B 85 VAL cc_start: 0.8663 (t) cc_final: 0.8396 (p) REVERT: B 92 MET cc_start: 0.8410 (mmm) cc_final: 0.7931 (mmm) REVERT: B 100 TYR cc_start: 0.6966 (t80) cc_final: 0.6258 (t80) REVERT: B 131 GLU cc_start: 0.7408 (tp30) cc_final: 0.7085 (tp30) REVERT: B 144 ASP cc_start: 0.8137 (m-30) cc_final: 0.7384 (m-30) REVERT: B 211 ASP cc_start: 0.7523 (t0) cc_final: 0.7232 (t0) REVERT: B 221 GLN cc_start: 0.8291 (pm20) cc_final: 0.7910 (pm20) REVERT: B 245 GLN cc_start: 0.7174 (tt0) cc_final: 0.6736 (tt0) REVERT: B 288 ARG cc_start: 0.7720 (mtt-85) cc_final: 0.7084 (mtt90) REVERT: B 299 LYS cc_start: 0.8080 (mmmm) cc_final: 0.7644 (mttp) REVERT: B 338 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7358 (tm-30) REVERT: B 403 ASP cc_start: 0.7285 (m-30) cc_final: 0.6841 (m-30) REVERT: B 411 ASP cc_start: 0.7236 (t0) cc_final: 0.6874 (m-30) REVERT: B 412 GLU cc_start: 0.6801 (tt0) cc_final: 0.6473 (tt0) REVERT: B 461 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7063 (mt-10) REVERT: B 492 ASP cc_start: 0.7815 (t0) cc_final: 0.7294 (t0) REVERT: B 544 ASN cc_start: 0.8464 (m-40) cc_final: 0.8192 (m-40) REVERT: B 585 TRP cc_start: 0.8455 (p-90) cc_final: 0.7562 (p-90) REVERT: B 599 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.6038 (ppt170) REVERT: B 634 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8535 (mm-40) REVERT: B 637 GLU cc_start: 0.7197 (tt0) cc_final: 0.6687 (tt0) REVERT: B 655 MET cc_start: 0.7811 (ttt) cc_final: 0.7510 (ttm) REVERT: B 667 GLU cc_start: 0.7126 (pm20) cc_final: 0.6698 (pm20) REVERT: B 677 LYS cc_start: 0.8377 (mtpt) cc_final: 0.7796 (mtpt) REVERT: B 768 MET cc_start: 0.4681 (ttm) cc_final: 0.4089 (ttm) REVERT: B 898 LEU cc_start: 0.6348 (tp) cc_final: 0.6075 (tp) REVERT: B 919 ASP cc_start: 0.8004 (m-30) cc_final: 0.7439 (t0) REVERT: B 997 ASP cc_start: 0.7406 (m-30) cc_final: 0.6968 (t0) REVERT: C 14 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7874 (mtp85) REVERT: C 15 ASP cc_start: 0.8083 (m-30) cc_final: 0.7609 (t0) REVERT: C 44 THR cc_start: 0.8916 (t) cc_final: 0.8048 (p) REVERT: C 45 ASP cc_start: 0.8593 (t70) cc_final: 0.8218 (t0) REVERT: C 46 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7686 (ttm110) REVERT: C 62 TRP cc_start: 0.8073 (t60) cc_final: 0.7637 (t60) REVERT: C 84 VAL cc_start: 0.8182 (t) cc_final: 0.7645 (p) REVERT: C 85 VAL cc_start: 0.8772 (t) cc_final: 0.8472 (p) REVERT: C 92 MET cc_start: 0.8204 (mmm) cc_final: 0.7693 (mmm) REVERT: C 100 TYR cc_start: 0.7200 (t80) cc_final: 0.6202 (t80) REVERT: C 136 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8085 (mp0) REVERT: C 144 ASP cc_start: 0.7987 (m-30) cc_final: 0.7174 (m-30) REVERT: C 187 MET cc_start: 0.8352 (ttp) cc_final: 0.8041 (ttp) REVERT: C 211 ASP cc_start: 0.7741 (t0) cc_final: 0.7344 (m-30) REVERT: C 237 ARG cc_start: 0.7335 (ttm-80) cc_final: 0.6983 (mtp85) REVERT: C 349 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7433 (tp) REVERT: C 403 ASP cc_start: 0.7164 (m-30) cc_final: 0.6607 (m-30) REVERT: C 492 ASP cc_start: 0.7737 (t0) cc_final: 0.7312 (t0) REVERT: C 515 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.7971 (m) REVERT: C 542 MET cc_start: 0.8305 (ptt) cc_final: 0.7931 (ptt) REVERT: C 599 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.6081 (ppt90) REVERT: C 634 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8379 (mm-40) REVERT: C 637 GLU cc_start: 0.7060 (tt0) cc_final: 0.6287 (tt0) REVERT: C 677 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7444 (mtpp) REVERT: C 693 GLN cc_start: 0.7167 (tp40) cc_final: 0.6378 (tp40) REVERT: C 721 ARG cc_start: 0.7596 (ttm-80) cc_final: 0.7100 (mtp-110) REVERT: C 756 TRP cc_start: 0.7436 (m-90) cc_final: 0.7139 (m-90) REVERT: C 792 ASP cc_start: 0.7821 (p0) cc_final: 0.7563 (p0) REVERT: C 808 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7491 (mm-30) REVERT: C 924 ASP cc_start: 0.8137 (m-30) cc_final: 0.7884 (t0) REVERT: C 997 ASP cc_start: 0.7184 (m-30) cc_final: 0.6900 (t0) REVERT: D 62 TRP cc_start: 0.7991 (t60) cc_final: 0.7596 (t60) REVERT: D 67 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7330 (mp0) REVERT: D 75 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7294 (tm-30) REVERT: D 84 VAL cc_start: 0.8150 (t) cc_final: 0.7600 (p) REVERT: D 85 VAL cc_start: 0.8632 (t) cc_final: 0.8380 (p) REVERT: D 100 TYR cc_start: 0.7097 (t80) cc_final: 0.6452 (t80) REVERT: D 131 GLU cc_start: 0.7371 (tp30) cc_final: 0.6888 (tp30) REVERT: D 132 SER cc_start: 0.8809 (m) cc_final: 0.8525 (t) REVERT: D 144 ASP cc_start: 0.8064 (m-30) cc_final: 0.7383 (m-30) REVERT: D 187 MET cc_start: 0.8445 (ttp) cc_final: 0.8154 (ttp) REVERT: D 211 ASP cc_start: 0.7699 (t0) cc_final: 0.7310 (m-30) REVERT: D 243 GLU cc_start: 0.6940 (tt0) cc_final: 0.6625 (tt0) REVERT: D 245 GLN cc_start: 0.7117 (tt0) cc_final: 0.6295 (tt0) REVERT: D 288 ARG cc_start: 0.7599 (mtt-85) cc_final: 0.6872 (mtt90) REVERT: D 403 ASP cc_start: 0.7453 (m-30) cc_final: 0.7027 (m-30) REVERT: D 411 ASP cc_start: 0.7077 (t0) cc_final: 0.6647 (m-30) REVERT: D 461 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7276 (mt-10) REVERT: D 492 ASP cc_start: 0.7751 (t0) cc_final: 0.7285 (t0) REVERT: D 599 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.6350 (pmt-80) REVERT: D 634 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8512 (mm-40) REVERT: D 655 MET cc_start: 0.7853 (ttt) cc_final: 0.7598 (ttm) REVERT: D 677 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8097 (mtpt) REVERT: D 693 GLN cc_start: 0.7071 (tp40) cc_final: 0.6782 (tp40) REVERT: D 709 SER cc_start: 0.7952 (t) cc_final: 0.7404 (p) REVERT: D 761 GLN cc_start: 0.6972 (mp10) cc_final: 0.6747 (mp10) REVERT: D 768 MET cc_start: 0.6285 (ttm) cc_final: 0.6077 (ttm) REVERT: D 924 ASP cc_start: 0.8267 (m-30) cc_final: 0.7960 (t0) REVERT: D 952 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7209 (ttm-80) REVERT: D 961 ARG cc_start: 0.7653 (tpt-90) cc_final: 0.7391 (ttt90) REVERT: D 997 ASP cc_start: 0.7369 (m-30) cc_final: 0.7112 (m-30) outliers start: 94 outliers final: 68 residues processed: 859 average time/residue: 0.2376 time to fit residues: 321.5898 Evaluate side-chains 862 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 785 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 977 HIS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1017 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 310 optimal weight: 0.0010 chunk 230 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 chunk 375 optimal weight: 3.9990 chunk 301 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 201 optimal weight: 0.0470 overall best weight: 1.8090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS A 840 HIS ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 HIS ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 840 HIS ** C 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D 840 HIS ** D 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.115903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098057 restraints weight = 57753.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101329 restraints weight = 27025.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.103587 restraints weight = 15750.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104969 restraints weight = 10459.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.106055 restraints weight = 7935.806| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33792 Z= 0.158 Angle : 0.651 8.120 46104 Z= 0.335 Chirality : 0.046 0.230 4820 Planarity : 0.004 0.037 6088 Dihedral : 4.669 37.793 4477 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.89 % Allowed : 17.53 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.13), residues: 4080 helix: -1.52 (0.29), residues: 340 sheet: 0.28 (0.14), residues: 1408 loop : -2.22 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 800 TYR 0.025 0.002 TYR B 161 PHE 0.016 0.001 PHE A 784 TRP 0.029 0.002 TRP B 153 HIS 0.014 0.001 HIS D1015 Details of bonding type rmsd covalent geometry : bond 0.00367 (33792) covalent geometry : angle 0.65085 (46104) hydrogen bonds : bond 0.04100 ( 856) hydrogen bonds : angle 4.97258 ( 2448) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 799 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7510 (ttm-80) REVERT: A 46 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7637 (ttm110) REVERT: A 62 TRP cc_start: 0.8193 (t60) cc_final: 0.7632 (t60) REVERT: A 67 GLU cc_start: 0.7716 (mp0) cc_final: 0.7501 (mp0) REVERT: A 75 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7166 (tm-30) REVERT: A 84 VAL cc_start: 0.8137 (t) cc_final: 0.7582 (p) REVERT: A 85 VAL cc_start: 0.8742 (t) cc_final: 0.8482 (p) REVERT: A 144 ASP cc_start: 0.7937 (m-30) cc_final: 0.7184 (m-30) REVERT: A 161 TYR cc_start: 0.7963 (t80) cc_final: 0.7623 (t80) REVERT: A 187 MET cc_start: 0.8252 (ttp) cc_final: 0.8024 (ttp) REVERT: A 243 GLU cc_start: 0.7047 (tt0) cc_final: 0.6809 (tt0) REVERT: A 288 ARG cc_start: 0.7984 (mtt-85) cc_final: 0.7499 (mtt-85) REVERT: A 334 GLU cc_start: 0.7290 (tp30) cc_final: 0.6691 (tm-30) REVERT: A 338 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7196 (tm-30) REVERT: A 412 GLU cc_start: 0.7277 (tt0) cc_final: 0.7030 (tt0) REVERT: A 492 ASP cc_start: 0.7880 (t0) cc_final: 0.7409 (t0) REVERT: A 599 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6701 (pmt-80) REVERT: A 603 MET cc_start: 0.5528 (mtp) cc_final: 0.5318 (mtp) REVERT: A 634 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8477 (mm-40) REVERT: A 637 GLU cc_start: 0.7318 (tt0) cc_final: 0.6402 (tt0) REVERT: A 655 MET cc_start: 0.7849 (ttt) cc_final: 0.7605 (ttm) REVERT: A 677 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7542 (mtpt) REVERT: A 693 GLN cc_start: 0.7097 (tp40) cc_final: 0.6413 (tp40) REVERT: A 699 ARG cc_start: 0.7026 (ptp90) cc_final: 0.6568 (ptp-170) REVERT: A 708 TRP cc_start: 0.8434 (p-90) cc_final: 0.8022 (p-90) REVERT: A 721 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7366 (mtp-110) REVERT: A 739 HIS cc_start: 0.7451 (t-90) cc_final: 0.7143 (t-90) REVERT: A 744 GLU cc_start: 0.8313 (pm20) cc_final: 0.7794 (pm20) REVERT: A 748 CYS cc_start: 0.8246 (m) cc_final: 0.7960 (m) REVERT: A 749 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7299 (tp) REVERT: A 756 TRP cc_start: 0.7438 (m-90) cc_final: 0.6957 (m-90) REVERT: A 792 ASP cc_start: 0.7727 (p0) cc_final: 0.7474 (p0) REVERT: A 935 ASN cc_start: 0.8881 (p0) cc_final: 0.8602 (p0) REVERT: A 945 ASN cc_start: 0.7375 (m-40) cc_final: 0.7148 (t0) REVERT: A 973 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7625 (ptm160) REVERT: A 974 HIS cc_start: 0.7650 (p-80) cc_final: 0.7171 (p-80) REVERT: A 975 LEU cc_start: 0.8658 (mt) cc_final: 0.8176 (mt) REVERT: A 997 ASP cc_start: 0.7208 (t0) cc_final: 0.6892 (t0) REVERT: B 62 TRP cc_start: 0.8093 (t60) cc_final: 0.7538 (t60) REVERT: B 67 GLU cc_start: 0.7646 (mp0) cc_final: 0.7407 (mp0) REVERT: B 84 VAL cc_start: 0.8323 (t) cc_final: 0.7781 (p) REVERT: B 85 VAL cc_start: 0.8700 (t) cc_final: 0.8427 (p) REVERT: B 92 MET cc_start: 0.8431 (mmm) cc_final: 0.8169 (mmm) REVERT: B 100 TYR cc_start: 0.7187 (t80) cc_final: 0.6432 (t80) REVERT: B 144 ASP cc_start: 0.8141 (m-30) cc_final: 0.7724 (m-30) REVERT: B 221 GLN cc_start: 0.8423 (pm20) cc_final: 0.8066 (pm20) REVERT: B 245 GLN cc_start: 0.7206 (tt0) cc_final: 0.6873 (tt0) REVERT: B 288 ARG cc_start: 0.7736 (mtt-85) cc_final: 0.7207 (mtt-85) REVERT: B 299 LYS cc_start: 0.8118 (mmmm) cc_final: 0.7689 (mttp) REVERT: B 338 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7441 (tm-30) REVERT: B 403 ASP cc_start: 0.7238 (m-30) cc_final: 0.6836 (m-30) REVERT: B 411 ASP cc_start: 0.7282 (t0) cc_final: 0.6943 (m-30) REVERT: B 412 GLU cc_start: 0.6856 (tt0) cc_final: 0.6447 (tt0) REVERT: B 492 ASP cc_start: 0.7913 (t0) cc_final: 0.7443 (t0) REVERT: B 542 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8232 (ptp) REVERT: B 585 TRP cc_start: 0.8555 (p-90) cc_final: 0.7765 (p-90) REVERT: B 599 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.6108 (ppt170) REVERT: B 634 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8625 (mm110) REVERT: B 637 GLU cc_start: 0.7208 (tt0) cc_final: 0.6777 (tt0) REVERT: B 655 MET cc_start: 0.7828 (ttt) cc_final: 0.7524 (ttm) REVERT: B 667 GLU cc_start: 0.7153 (pm20) cc_final: 0.6668 (pm20) REVERT: B 677 LYS cc_start: 0.8429 (mtpt) cc_final: 0.7833 (mtpt) REVERT: B 693 GLN cc_start: 0.7027 (tp40) cc_final: 0.6276 (tp40) REVERT: B 768 MET cc_start: 0.4736 (ttm) cc_final: 0.4159 (ttm) REVERT: B 898 LEU cc_start: 0.6441 (tp) cc_final: 0.6149 (tp) REVERT: B 919 ASP cc_start: 0.8076 (m-30) cc_final: 0.7383 (t0) REVERT: B 997 ASP cc_start: 0.7393 (m-30) cc_final: 0.6930 (t0) REVERT: B 1022 GLN cc_start: 0.6837 (tm-30) cc_final: 0.6431 (tm-30) REVERT: C 15 ASP cc_start: 0.8273 (m-30) cc_final: 0.7838 (t0) REVERT: C 44 THR cc_start: 0.8842 (t) cc_final: 0.8112 (p) REVERT: C 45 ASP cc_start: 0.8569 (t70) cc_final: 0.8147 (t0) REVERT: C 46 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7870 (ttm110) REVERT: C 62 TRP cc_start: 0.8236 (t60) cc_final: 0.7758 (t60) REVERT: C 84 VAL cc_start: 0.8280 (t) cc_final: 0.7728 (p) REVERT: C 85 VAL cc_start: 0.8787 (t) cc_final: 0.8496 (p) REVERT: C 92 MET cc_start: 0.8210 (mmm) cc_final: 0.7695 (mmm) REVERT: C 100 TYR cc_start: 0.7294 (t80) cc_final: 0.6300 (t80) REVERT: C 131 GLU cc_start: 0.7141 (tp30) cc_final: 0.6774 (tp30) REVERT: C 144 ASP cc_start: 0.8009 (m-30) cc_final: 0.7238 (m-30) REVERT: C 161 TYR cc_start: 0.7676 (t80) cc_final: 0.7303 (t80) REVERT: C 187 MET cc_start: 0.8343 (ttp) cc_final: 0.8060 (ttp) REVERT: C 211 ASP cc_start: 0.7794 (t0) cc_final: 0.7453 (m-30) REVERT: C 237 ARG cc_start: 0.7397 (ttm-80) cc_final: 0.6992 (mtp85) REVERT: C 349 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7469 (tp) REVERT: C 403 ASP cc_start: 0.7204 (m-30) cc_final: 0.6646 (m-30) REVERT: C 492 ASP cc_start: 0.7826 (t0) cc_final: 0.7450 (t0) REVERT: C 515 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8109 (m) REVERT: C 599 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6508 (ppt170) REVERT: C 634 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8452 (mm-40) REVERT: C 637 GLU cc_start: 0.7072 (tt0) cc_final: 0.6366 (tt0) REVERT: C 677 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7533 (mtpp) REVERT: C 693 GLN cc_start: 0.7249 (tp40) cc_final: 0.6558 (tp40) REVERT: C 708 TRP cc_start: 0.8338 (p-90) cc_final: 0.6989 (p-90) REVERT: C 721 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7230 (mtp-110) REVERT: C 749 ILE cc_start: 0.7088 (tp) cc_final: 0.6606 (pt) REVERT: C 756 TRP cc_start: 0.7408 (m-90) cc_final: 0.7036 (m-90) REVERT: C 792 ASP cc_start: 0.7811 (p0) cc_final: 0.7531 (p0) REVERT: C 808 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7525 (mm-30) REVERT: C 908 ASP cc_start: 0.7895 (t0) cc_final: 0.7661 (t0) REVERT: C 924 ASP cc_start: 0.8159 (m-30) cc_final: 0.7893 (t0) REVERT: C 997 ASP cc_start: 0.7167 (m-30) cc_final: 0.6885 (t0) REVERT: D 62 TRP cc_start: 0.8144 (t60) cc_final: 0.7684 (t60) REVERT: D 67 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7382 (mp0) REVERT: D 75 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7265 (tm-30) REVERT: D 84 VAL cc_start: 0.8211 (t) cc_final: 0.7695 (p) REVERT: D 85 VAL cc_start: 0.8706 (t) cc_final: 0.8500 (p) REVERT: D 100 TYR cc_start: 0.7282 (t80) cc_final: 0.6499 (t80) REVERT: D 131 GLU cc_start: 0.7551 (tp30) cc_final: 0.6973 (tp30) REVERT: D 132 SER cc_start: 0.8714 (m) cc_final: 0.8455 (t) REVERT: D 144 ASP cc_start: 0.8071 (m-30) cc_final: 0.7379 (m-30) REVERT: D 170 GLU cc_start: 0.6878 (pm20) cc_final: 0.6673 (pm20) REVERT: D 187 MET cc_start: 0.8468 (ttp) cc_final: 0.8201 (ttp) REVERT: D 211 ASP cc_start: 0.7761 (t0) cc_final: 0.7401 (m-30) REVERT: D 241 GLU cc_start: 0.7078 (pt0) cc_final: 0.6771 (mt-10) REVERT: D 243 GLU cc_start: 0.6959 (tt0) cc_final: 0.6620 (tt0) REVERT: D 245 GLN cc_start: 0.7154 (tt0) cc_final: 0.6592 (tt0) REVERT: D 288 ARG cc_start: 0.7708 (mtt-85) cc_final: 0.7169 (mtt90) REVERT: D 369 GLU cc_start: 0.8115 (tp30) cc_final: 0.7909 (tp30) REVERT: D 403 ASP cc_start: 0.7421 (m-30) cc_final: 0.6907 (m-30) REVERT: D 411 ASP cc_start: 0.7165 (t0) cc_final: 0.6697 (m-30) REVERT: D 492 ASP cc_start: 0.7845 (t0) cc_final: 0.7435 (t0) REVERT: D 599 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6696 (pmt-80) REVERT: D 634 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8546 (mm-40) REVERT: D 655 MET cc_start: 0.7867 (ttt) cc_final: 0.7623 (ttm) REVERT: D 677 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8157 (mtpt) REVERT: D 693 GLN cc_start: 0.7145 (tp-100) cc_final: 0.6754 (tp40) REVERT: D 721 ARG cc_start: 0.7759 (ttm-80) cc_final: 0.7413 (tpp80) REVERT: D 924 ASP cc_start: 0.8298 (m-30) cc_final: 0.7986 (t0) REVERT: D 952 ARG cc_start: 0.7639 (ttm-80) cc_final: 0.7309 (ttm-80) outliers start: 101 outliers final: 79 residues processed: 853 average time/residue: 0.2401 time to fit residues: 322.0499 Evaluate side-chains 876 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 788 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 977 HIS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 966 GLN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 925 MET Chi-restraints excluded: chain D residue 959 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 225 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 335 optimal weight: 7.9990 chunk 169 optimal weight: 0.0570 chunk 369 optimal weight: 3.9990 chunk 258 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 277 optimal weight: 20.0000 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 HIS ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 GLN B 93 HIS B 216 HIS ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN B 604 ASN ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 HIS ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 GLN ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 ASN C 840 HIS ** C 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 840 HIS ** D 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.094312 restraints weight = 58019.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.097644 restraints weight = 27165.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099802 restraints weight = 15569.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101159 restraints weight = 10375.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102192 restraints weight = 7870.347| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 33792 Z= 0.265 Angle : 0.764 11.397 46104 Z= 0.399 Chirality : 0.050 0.196 4820 Planarity : 0.005 0.072 6088 Dihedral : 5.267 48.148 4477 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.23 % Allowed : 17.65 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.13), residues: 4080 helix: -1.57 (0.28), residues: 332 sheet: 0.22 (0.14), residues: 1356 loop : -2.47 (0.11), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 721 TYR 0.028 0.002 TYR B 161 PHE 0.021 0.002 PHE C 549 TRP 0.032 0.002 TRP C 842 HIS 0.021 0.002 HIS D1015 Details of bonding type rmsd covalent geometry : bond 0.00618 (33792) covalent geometry : angle 0.76446 (46104) hydrogen bonds : bond 0.05689 ( 856) hydrogen bonds : angle 5.45553 ( 2448) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 799 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TRP cc_start: 0.8402 (t60) cc_final: 0.7963 (t60) REVERT: A 67 GLU cc_start: 0.7813 (mp0) cc_final: 0.7592 (mp0) REVERT: A 75 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 84 VAL cc_start: 0.8249 (t) cc_final: 0.7746 (p) REVERT: A 85 VAL cc_start: 0.8771 (t) cc_final: 0.8530 (p) REVERT: A 92 MET cc_start: 0.8218 (mmm) cc_final: 0.7877 (mmm) REVERT: A 100 TYR cc_start: 0.7464 (t80) cc_final: 0.6378 (t80) REVERT: A 131 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7423 (tm-30) REVERT: A 136 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8230 (mp0) REVERT: A 144 ASP cc_start: 0.7969 (m-30) cc_final: 0.7224 (m-30) REVERT: A 161 TYR cc_start: 0.8028 (t80) cc_final: 0.7716 (t80) REVERT: A 243 GLU cc_start: 0.7124 (tt0) cc_final: 0.6836 (tt0) REVERT: A 288 ARG cc_start: 0.8053 (mtt-85) cc_final: 0.7731 (mtt-85) REVERT: A 324 GLU cc_start: 0.7679 (mp0) cc_final: 0.7377 (mp0) REVERT: A 412 GLU cc_start: 0.7379 (tt0) cc_final: 0.7176 (tt0) REVERT: A 492 ASP cc_start: 0.8094 (t0) cc_final: 0.7704 (t0) REVERT: A 585 TRP cc_start: 0.8814 (p-90) cc_final: 0.8004 (p90) REVERT: A 599 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.5458 (pmt-80) REVERT: A 634 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8522 (mm-40) REVERT: A 637 GLU cc_start: 0.7323 (tt0) cc_final: 0.6409 (tt0) REVERT: A 655 MET cc_start: 0.7869 (ttt) cc_final: 0.7603 (ttm) REVERT: A 677 LYS cc_start: 0.8298 (mtpt) cc_final: 0.7579 (mtpt) REVERT: A 693 GLN cc_start: 0.7209 (tp40) cc_final: 0.6515 (tp40) REVERT: A 699 ARG cc_start: 0.7121 (ptp90) cc_final: 0.6698 (ptp-170) REVERT: A 708 TRP cc_start: 0.8427 (p-90) cc_final: 0.8020 (p-90) REVERT: A 739 HIS cc_start: 0.7711 (t-90) cc_final: 0.7452 (t-90) REVERT: A 761 GLN cc_start: 0.7122 (mp10) cc_final: 0.6868 (mp10) REVERT: A 775 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7554 (mm110) REVERT: A 792 ASP cc_start: 0.7688 (p0) cc_final: 0.7433 (p0) REVERT: A 973 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7718 (ptm160) REVERT: A 974 HIS cc_start: 0.7670 (p-80) cc_final: 0.6917 (p90) REVERT: A 975 LEU cc_start: 0.8669 (mt) cc_final: 0.8307 (mm) REVERT: A 997 ASP cc_start: 0.7508 (t0) cc_final: 0.7136 (t0) REVERT: A 1019 VAL cc_start: 0.8647 (t) cc_final: 0.8288 (p) REVERT: B 2 MET cc_start: 0.5691 (tmm) cc_final: 0.5438 (tmm) REVERT: B 15 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7870 (t0) REVERT: B 62 TRP cc_start: 0.8245 (t60) cc_final: 0.7681 (t60) REVERT: B 84 VAL cc_start: 0.8314 (t) cc_final: 0.7805 (p) REVERT: B 85 VAL cc_start: 0.8696 (t) cc_final: 0.8433 (p) REVERT: B 92 MET cc_start: 0.8432 (mmm) cc_final: 0.8191 (mmm) REVERT: B 100 TYR cc_start: 0.7516 (t80) cc_final: 0.6693 (t80) REVERT: B 144 ASP cc_start: 0.8145 (m-30) cc_final: 0.7708 (m-30) REVERT: B 221 GLN cc_start: 0.8481 (pm20) cc_final: 0.8175 (pm20) REVERT: B 237 ARG cc_start: 0.7420 (mtp85) cc_final: 0.6438 (mtp85) REVERT: B 245 GLN cc_start: 0.7245 (tt0) cc_final: 0.6869 (tt0) REVERT: B 288 ARG cc_start: 0.7790 (mtt-85) cc_final: 0.7253 (mtt-85) REVERT: B 403 ASP cc_start: 0.7271 (m-30) cc_final: 0.6913 (m-30) REVERT: B 585 TRP cc_start: 0.8712 (p-90) cc_final: 0.7404 (p-90) REVERT: B 599 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6215 (ppt170) REVERT: B 603 MET cc_start: 0.6079 (mtp) cc_final: 0.5841 (mtp) REVERT: B 634 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8686 (mm110) REVERT: B 637 GLU cc_start: 0.7265 (tt0) cc_final: 0.6712 (tt0) REVERT: B 655 MET cc_start: 0.7870 (ttt) cc_final: 0.7568 (ttm) REVERT: B 672 VAL cc_start: 0.8674 (m) cc_final: 0.8442 (t) REVERT: B 677 LYS cc_start: 0.8522 (mtpt) cc_final: 0.7750 (mtpt) REVERT: B 708 TRP cc_start: 0.8291 (p-90) cc_final: 0.7770 (p-90) REVERT: B 721 ARG cc_start: 0.7662 (mtp-110) cc_final: 0.7422 (mtp-110) REVERT: B 739 HIS cc_start: 0.7612 (t-90) cc_final: 0.7326 (t-90) REVERT: B 761 GLN cc_start: 0.7231 (mp10) cc_final: 0.6950 (mp10) REVERT: B 768 MET cc_start: 0.4819 (ttm) cc_final: 0.4263 (ttm) REVERT: B 837 THR cc_start: 0.8016 (p) cc_final: 0.7672 (t) REVERT: B 898 LEU cc_start: 0.6338 (tp) cc_final: 0.6126 (tp) REVERT: B 908 ASP cc_start: 0.7818 (t0) cc_final: 0.7468 (t0) REVERT: B 919 ASP cc_start: 0.8047 (m-30) cc_final: 0.7369 (t0) REVERT: B 983 TRP cc_start: 0.7974 (m100) cc_final: 0.7702 (m100) REVERT: B 997 ASP cc_start: 0.7350 (m-30) cc_final: 0.6796 (t0) REVERT: B 1022 GLN cc_start: 0.6988 (tm-30) cc_final: 0.6617 (tm-30) REVERT: C 15 ASP cc_start: 0.8297 (m-30) cc_final: 0.7886 (t0) REVERT: C 44 THR cc_start: 0.8820 (t) cc_final: 0.8535 (p) REVERT: C 45 ASP cc_start: 0.8596 (t70) cc_final: 0.8114 (t0) REVERT: C 62 TRP cc_start: 0.8402 (t60) cc_final: 0.7884 (t60) REVERT: C 84 VAL cc_start: 0.8355 (t) cc_final: 0.7840 (p) REVERT: C 85 VAL cc_start: 0.8831 (t) cc_final: 0.8590 (p) REVERT: C 92 MET cc_start: 0.8231 (mmm) cc_final: 0.7978 (mmt) REVERT: C 100 TYR cc_start: 0.7518 (t80) cc_final: 0.6406 (t80) REVERT: C 144 ASP cc_start: 0.8043 (m-30) cc_final: 0.7247 (m-30) REVERT: C 161 TYR cc_start: 0.7797 (t80) cc_final: 0.7380 (t80) REVERT: C 167 LEU cc_start: 0.7528 (mm) cc_final: 0.7127 (mp) REVERT: C 211 ASP cc_start: 0.7843 (t0) cc_final: 0.7356 (m-30) REVERT: C 237 ARG cc_start: 0.7397 (ttm-80) cc_final: 0.7169 (ttm-80) REVERT: C 245 GLN cc_start: 0.6747 (OUTLIER) cc_final: 0.6537 (tt0) REVERT: C 349 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7549 (tp) REVERT: C 403 ASP cc_start: 0.7202 (m-30) cc_final: 0.6675 (m-30) REVERT: C 429 ASP cc_start: 0.8598 (t70) cc_final: 0.8333 (t0) REVERT: C 492 ASP cc_start: 0.7969 (t0) cc_final: 0.7683 (t0) REVERT: C 515 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8228 (m) REVERT: C 599 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6376 (pmt-80) REVERT: C 634 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8593 (mm-40) REVERT: C 637 GLU cc_start: 0.7133 (tt0) cc_final: 0.6255 (tt0) REVERT: C 677 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7518 (mtpt) REVERT: C 693 GLN cc_start: 0.7415 (tp40) cc_final: 0.6580 (tp40) REVERT: C 708 TRP cc_start: 0.8305 (p-90) cc_final: 0.7065 (p-90) REVERT: C 721 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7288 (mtp-110) REVERT: C 761 GLN cc_start: 0.7356 (mm-40) cc_final: 0.6907 (mp10) REVERT: C 792 ASP cc_start: 0.7726 (p0) cc_final: 0.7454 (p0) REVERT: C 808 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7504 (mm-30) REVERT: C 824 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 908 ASP cc_start: 0.7999 (t0) cc_final: 0.7783 (t0) REVERT: C 924 ASP cc_start: 0.8207 (m-30) cc_final: 0.7875 (t0) REVERT: C 997 ASP cc_start: 0.7142 (m-30) cc_final: 0.6655 (t0) REVERT: C 1019 VAL cc_start: 0.8541 (t) cc_final: 0.8158 (p) REVERT: D 15 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7834 (t0) REVERT: D 62 TRP cc_start: 0.8317 (t60) cc_final: 0.7898 (t60) REVERT: D 67 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7521 (mp0) REVERT: D 75 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7312 (tm-30) REVERT: D 84 VAL cc_start: 0.8287 (t) cc_final: 0.7786 (p) REVERT: D 100 TYR cc_start: 0.7380 (t80) cc_final: 0.6408 (t80) REVERT: D 144 ASP cc_start: 0.8134 (m-30) cc_final: 0.7517 (m-30) REVERT: D 163 GLN cc_start: 0.7217 (tp-100) cc_final: 0.6998 (tp40) REVERT: D 170 GLU cc_start: 0.7006 (pm20) cc_final: 0.6735 (pm20) REVERT: D 181 GLU cc_start: 0.8323 (pm20) cc_final: 0.8110 (pm20) REVERT: D 187 MET cc_start: 0.8452 (ttp) cc_final: 0.8237 (ttp) REVERT: D 192 SER cc_start: 0.8223 (t) cc_final: 0.7776 (t) REVERT: D 211 ASP cc_start: 0.7809 (t0) cc_final: 0.7458 (m-30) REVERT: D 241 GLU cc_start: 0.7092 (pt0) cc_final: 0.6813 (mt-10) REVERT: D 243 GLU cc_start: 0.6983 (tt0) cc_final: 0.6610 (tt0) REVERT: D 245 GLN cc_start: 0.7144 (tt0) cc_final: 0.6763 (tt0) REVERT: D 288 ARG cc_start: 0.7795 (mtt-85) cc_final: 0.7487 (mtt-85) REVERT: D 369 GLU cc_start: 0.8206 (tp30) cc_final: 0.7969 (tp30) REVERT: D 403 ASP cc_start: 0.7528 (m-30) cc_final: 0.6995 (m-30) REVERT: D 492 ASP cc_start: 0.7970 (t0) cc_final: 0.7669 (t0) REVERT: D 599 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.5624 (pmt-80) REVERT: D 634 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8569 (mm-40) REVERT: D 655 MET cc_start: 0.7857 (ttt) cc_final: 0.7608 (ttm) REVERT: D 677 LYS cc_start: 0.8369 (mtpt) cc_final: 0.7910 (mtpt) REVERT: D 693 GLN cc_start: 0.7230 (tp-100) cc_final: 0.6884 (tp40) REVERT: D 721 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.7399 (tpp80) REVERT: D 874 SER cc_start: 0.9288 (m) cc_final: 0.8501 (t) REVERT: D 924 ASP cc_start: 0.8285 (m-30) cc_final: 0.8074 (t0) REVERT: D 952 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7397 (ttm110) REVERT: D 997 ASP cc_start: 0.7360 (m-30) cc_final: 0.7047 (m-30) REVERT: D 1019 VAL cc_start: 0.8653 (t) cc_final: 0.8263 (p) outliers start: 113 outliers final: 85 residues processed: 860 average time/residue: 0.2412 time to fit residues: 324.6059 Evaluate side-chains 882 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 786 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 950 GLN Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 977 HIS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 925 MET Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 1017 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 64 optimal weight: 4.9990 chunk 357 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 263 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 HIS ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 GLN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 HIS ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 840 HIS ** C 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 ASN D 840 HIS ** D 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.097964 restraints weight = 57752.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101343 restraints weight = 27081.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.103565 restraints weight = 15478.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105033 restraints weight = 10257.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105944 restraints weight = 7652.989| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33792 Z= 0.127 Angle : 0.672 10.736 46104 Z= 0.342 Chirality : 0.046 0.298 4820 Planarity : 0.004 0.046 6088 Dihedral : 4.849 47.006 4477 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.37 % Allowed : 19.39 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.13), residues: 4080 helix: -1.50 (0.29), residues: 340 sheet: 0.21 (0.14), residues: 1392 loop : -2.27 (0.12), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 800 TYR 0.023 0.001 TYR B 161 PHE 0.012 0.001 PHE A 850 TRP 0.026 0.002 TRP A 842 HIS 0.012 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00293 (33792) covalent geometry : angle 0.67203 (46104) hydrogen bonds : bond 0.03652 ( 856) hydrogen bonds : angle 5.00302 ( 2448) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 810 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8439 (mtm110) cc_final: 0.7962 (ttm-80) REVERT: A 46 ARG cc_start: 0.8256 (tpp80) cc_final: 0.7723 (ttm110) REVERT: A 62 TRP cc_start: 0.8208 (t60) cc_final: 0.7698 (t60) REVERT: A 67 GLU cc_start: 0.7725 (mp0) cc_final: 0.7513 (mp0) REVERT: A 75 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7218 (tm-30) REVERT: A 84 VAL cc_start: 0.8194 (t) cc_final: 0.7643 (p) REVERT: A 85 VAL cc_start: 0.8731 (t) cc_final: 0.8476 (p) REVERT: A 129 VAL cc_start: 0.8378 (p) cc_final: 0.8169 (t) REVERT: A 131 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 136 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8187 (mp0) REVERT: A 144 ASP cc_start: 0.7932 (m-30) cc_final: 0.7173 (m-30) REVERT: A 161 TYR cc_start: 0.7992 (t80) cc_final: 0.7718 (t80) REVERT: A 237 ARG cc_start: 0.7297 (mtp85) cc_final: 0.6993 (mtp85) REVERT: A 243 GLU cc_start: 0.7061 (tt0) cc_final: 0.6750 (tt0) REVERT: A 245 GLN cc_start: 0.6730 (tp40) cc_final: 0.6367 (tp40) REVERT: A 338 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7253 (tm-30) REVERT: A 367 MET cc_start: 0.7589 (mmm) cc_final: 0.7349 (mmm) REVERT: A 412 GLU cc_start: 0.7235 (tt0) cc_final: 0.7027 (tt0) REVERT: A 492 ASP cc_start: 0.7952 (t0) cc_final: 0.7485 (t0) REVERT: A 585 TRP cc_start: 0.8847 (p-90) cc_final: 0.7638 (p-90) REVERT: A 599 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6616 (pmt-80) REVERT: A 634 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8279 (mm110) REVERT: A 637 GLU cc_start: 0.7374 (tt0) cc_final: 0.6352 (tt0) REVERT: A 655 MET cc_start: 0.7799 (ttt) cc_final: 0.7534 (ttm) REVERT: A 677 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7504 (mtpt) REVERT: A 693 GLN cc_start: 0.7088 (tp40) cc_final: 0.6698 (tp40) REVERT: A 699 ARG cc_start: 0.6857 (ptp90) cc_final: 0.6402 (ptp-170) REVERT: A 708 TRP cc_start: 0.8434 (p-90) cc_final: 0.8004 (p-90) REVERT: A 749 ILE cc_start: 0.7403 (tp) cc_final: 0.6705 (pt) REVERT: A 756 TRP cc_start: 0.7422 (m-90) cc_final: 0.6862 (m-90) REVERT: A 761 GLN cc_start: 0.7028 (mp10) cc_final: 0.6792 (mp10) REVERT: A 792 ASP cc_start: 0.7720 (p0) cc_final: 0.7433 (p0) REVERT: A 890 GLN cc_start: 0.7329 (mm-40) cc_final: 0.6850 (mm-40) REVERT: A 935 ASN cc_start: 0.9030 (p0) cc_final: 0.8715 (p0) REVERT: A 945 ASN cc_start: 0.7494 (m-40) cc_final: 0.7210 (t0) REVERT: A 974 HIS cc_start: 0.7656 (p-80) cc_final: 0.7248 (p-80) REVERT: A 975 LEU cc_start: 0.8644 (mt) cc_final: 0.8193 (mt) REVERT: A 997 ASP cc_start: 0.7446 (t0) cc_final: 0.7049 (t0) REVERT: A 1019 VAL cc_start: 0.8584 (t) cc_final: 0.8202 (p) REVERT: B 15 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7850 (t0) REVERT: B 62 TRP cc_start: 0.8046 (t60) cc_final: 0.7509 (t60) REVERT: B 84 VAL cc_start: 0.8250 (t) cc_final: 0.7724 (p) REVERT: B 85 VAL cc_start: 0.8677 (t) cc_final: 0.8422 (p) REVERT: B 92 MET cc_start: 0.8430 (mmm) cc_final: 0.8187 (mmm) REVERT: B 100 TYR cc_start: 0.7258 (t80) cc_final: 0.6474 (t80) REVERT: B 136 GLU cc_start: 0.8381 (mp0) cc_final: 0.7954 (mp0) REVERT: B 144 ASP cc_start: 0.8116 (m-30) cc_final: 0.7360 (m-30) REVERT: B 221 GLN cc_start: 0.8420 (pm20) cc_final: 0.8135 (pm20) REVERT: B 237 ARG cc_start: 0.7394 (mtp85) cc_final: 0.6433 (mtp85) REVERT: B 245 GLN cc_start: 0.7201 (tt0) cc_final: 0.6053 (tt0) REVERT: B 288 ARG cc_start: 0.7766 (mtt-85) cc_final: 0.6943 (mtt-85) REVERT: B 403 ASP cc_start: 0.7248 (m-30) cc_final: 0.6844 (m-30) REVERT: B 411 ASP cc_start: 0.7240 (t0) cc_final: 0.6948 (m-30) REVERT: B 412 GLU cc_start: 0.6959 (tt0) cc_final: 0.6731 (pt0) REVERT: B 473 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7737 (tpt170) REVERT: B 492 ASP cc_start: 0.7944 (t0) cc_final: 0.7507 (t0) REVERT: B 544 ASN cc_start: 0.8418 (m-40) cc_final: 0.8108 (m-40) REVERT: B 585 TRP cc_start: 0.8724 (p-90) cc_final: 0.7851 (p-90) REVERT: B 599 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.6102 (ppt170) REVERT: B 603 MET cc_start: 0.5551 (mtp) cc_final: 0.5235 (mtp) REVERT: B 634 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8623 (mm110) REVERT: B 655 MET cc_start: 0.7812 (ttt) cc_final: 0.7513 (ttm) REVERT: B 667 GLU cc_start: 0.7152 (pm20) cc_final: 0.6851 (pm20) REVERT: B 693 GLN cc_start: 0.6523 (tp40) cc_final: 0.6074 (tm-30) REVERT: B 708 TRP cc_start: 0.8285 (p-90) cc_final: 0.7747 (p-90) REVERT: B 739 HIS cc_start: 0.7573 (t-90) cc_final: 0.7355 (t-90) REVERT: B 761 GLN cc_start: 0.6962 (mp10) cc_final: 0.6761 (mp10) REVERT: B 898 LEU cc_start: 0.6385 (tp) cc_final: 0.6185 (tp) REVERT: B 908 ASP cc_start: 0.7831 (t0) cc_final: 0.7502 (t0) REVERT: B 919 ASP cc_start: 0.7996 (m-30) cc_final: 0.7428 (t0) REVERT: B 983 TRP cc_start: 0.7964 (m100) cc_final: 0.7683 (m100) REVERT: B 997 ASP cc_start: 0.7389 (m-30) cc_final: 0.6918 (t0) REVERT: C 15 ASP cc_start: 0.8255 (m-30) cc_final: 0.7855 (t0) REVERT: C 44 THR cc_start: 0.8719 (t) cc_final: 0.8133 (p) REVERT: C 45 ASP cc_start: 0.8496 (t70) cc_final: 0.8094 (t0) REVERT: C 46 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.8014 (ttm110) REVERT: C 62 TRP cc_start: 0.8185 (t60) cc_final: 0.7732 (t60) REVERT: C 84 VAL cc_start: 0.8236 (t) cc_final: 0.7749 (p) REVERT: C 85 VAL cc_start: 0.8759 (t) cc_final: 0.8489 (p) REVERT: C 92 MET cc_start: 0.8223 (mmm) cc_final: 0.7712 (mmm) REVERT: C 100 TYR cc_start: 0.7321 (t80) cc_final: 0.6272 (t80) REVERT: C 144 ASP cc_start: 0.7979 (m-30) cc_final: 0.7179 (m-30) REVERT: C 161 TYR cc_start: 0.7679 (t80) cc_final: 0.7325 (t80) REVERT: C 211 ASP cc_start: 0.7781 (t0) cc_final: 0.7416 (m-30) REVERT: C 237 ARG cc_start: 0.7325 (ttm-80) cc_final: 0.6932 (mtp85) REVERT: C 245 GLN cc_start: 0.6720 (OUTLIER) cc_final: 0.6224 (tt0) REVERT: C 349 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7427 (tp) REVERT: C 403 ASP cc_start: 0.7162 (m-30) cc_final: 0.6635 (m-30) REVERT: C 492 ASP cc_start: 0.7811 (t0) cc_final: 0.7449 (t0) REVERT: C 515 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8101 (m) REVERT: C 634 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8498 (mm-40) REVERT: C 637 GLU cc_start: 0.7101 (tt0) cc_final: 0.6342 (tt0) REVERT: C 677 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7450 (mtpp) REVERT: C 693 GLN cc_start: 0.7293 (tp40) cc_final: 0.6426 (tp40) REVERT: C 708 TRP cc_start: 0.8321 (p-90) cc_final: 0.7010 (p-90) REVERT: C 721 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7147 (mtp-110) REVERT: C 749 ILE cc_start: 0.7028 (tp) cc_final: 0.6640 (pt) REVERT: C 756 TRP cc_start: 0.7399 (m-90) cc_final: 0.7033 (m-90) REVERT: C 757 GLN cc_start: 0.7646 (mt0) cc_final: 0.7254 (mt0) REVERT: C 761 GLN cc_start: 0.7361 (mm-40) cc_final: 0.6943 (mp10) REVERT: C 790 ASP cc_start: 0.7363 (t0) cc_final: 0.7028 (t0) REVERT: C 792 ASP cc_start: 0.7765 (p0) cc_final: 0.7508 (p0) REVERT: C 808 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7456 (mm-30) REVERT: C 924 ASP cc_start: 0.8181 (m-30) cc_final: 0.7863 (t0) REVERT: C 997 ASP cc_start: 0.7143 (m-30) cc_final: 0.6885 (t0) REVERT: D 15 ASP cc_start: 0.8295 (m-30) cc_final: 0.7825 (t0) REVERT: D 62 TRP cc_start: 0.8127 (t60) cc_final: 0.7707 (t60) REVERT: D 67 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7477 (mp0) REVERT: D 75 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7293 (tm-30) REVERT: D 84 VAL cc_start: 0.8172 (t) cc_final: 0.7630 (p) REVERT: D 100 TYR cc_start: 0.7155 (t80) cc_final: 0.6287 (t80) REVERT: D 144 ASP cc_start: 0.8089 (m-30) cc_final: 0.7423 (m-30) REVERT: D 187 MET cc_start: 0.8456 (ttp) cc_final: 0.8221 (ttp) REVERT: D 211 ASP cc_start: 0.7726 (t0) cc_final: 0.7314 (m-30) REVERT: D 241 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6780 (mt-10) REVERT: D 243 GLU cc_start: 0.6962 (tt0) cc_final: 0.6584 (tt0) REVERT: D 245 GLN cc_start: 0.7054 (tt0) cc_final: 0.6628 (tt0) REVERT: D 288 ARG cc_start: 0.7711 (mtt-85) cc_final: 0.7441 (mtt-85) REVERT: D 369 GLU cc_start: 0.8128 (tp30) cc_final: 0.7915 (tp30) REVERT: D 403 ASP cc_start: 0.7479 (m-30) cc_final: 0.7193 (m-30) REVERT: D 492 ASP cc_start: 0.7889 (t0) cc_final: 0.7534 (t0) REVERT: D 599 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6642 (pmt-80) REVERT: D 634 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8564 (mm110) REVERT: D 655 MET cc_start: 0.7810 (ttt) cc_final: 0.7574 (ttm) REVERT: D 677 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7844 (mtpt) REVERT: D 874 SER cc_start: 0.9258 (m) cc_final: 0.8828 (p) REVERT: D 924 ASP cc_start: 0.8231 (m-30) cc_final: 0.7886 (t0) REVERT: D 952 ARG cc_start: 0.7582 (ttm-80) cc_final: 0.7352 (ttm110) outliers start: 83 outliers final: 64 residues processed: 854 average time/residue: 0.2418 time to fit residues: 323.1125 Evaluate side-chains 867 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 795 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 977 HIS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 925 MET Chi-restraints excluded: chain D residue 959 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 362 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 284 optimal weight: 0.1980 chunk 46 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 8.9990 chunk 256 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 281 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 HIS ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 GLN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 HIS ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 HIS ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 ASN C 840 HIS ** C 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 ASN D 840 HIS ** D 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098287 restraints weight = 57397.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101632 restraints weight = 26955.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103734 restraints weight = 15491.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.105246 restraints weight = 10412.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106243 restraints weight = 7790.890| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33792 Z= 0.146 Angle : 0.682 10.942 46104 Z= 0.348 Chirality : 0.046 0.255 4820 Planarity : 0.004 0.044 6088 Dihedral : 4.809 47.713 4477 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.35 % Allowed : 19.51 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.13), residues: 4080 helix: -1.39 (0.29), residues: 340 sheet: 0.24 (0.14), residues: 1392 loop : -2.24 (0.12), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 721 TYR 0.024 0.002 TYR B 161 PHE 0.012 0.001 PHE C 549 TRP 0.025 0.002 TRP C 261 HIS 0.012 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00340 (33792) covalent geometry : angle 0.68191 (46104) hydrogen bonds : bond 0.03952 ( 856) hydrogen bonds : angle 4.96235 ( 2448) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6600.87 seconds wall clock time: 114 minutes 12.19 seconds (6852.19 seconds total)