Starting phenix.real_space_refine on Fri May 30 01:43:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vt0_43514/05_2025/8vt0_43514.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vt0_43514/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vt0_43514/05_2025/8vt0_43514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vt0_43514/05_2025/8vt0_43514.map" model { file = "/net/cci-nas-00/data/ceres_data/8vt0_43514/05_2025/8vt0_43514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vt0_43514/05_2025/8vt0_43514.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, D Time building chain proxies: 22.81, per 1000 atoms: 0.69 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: 7.89 Conformation dependent library (CDL) restraints added in 4.2 seconds 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: 4.88 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: 14.42 Time building geometry restraints manager: 9.31 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: 0.25 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.400 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: 1.160 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 75.190 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.056 0.004 TRP A 58 HIS 0.014 0.003 HIS B 972 PHE 0.024 0.004 PHE C 989 TYR 0.029 0.003 TYR A 538 ARG 0.012 0.001 ARG A 166 Details of bonding type rmsd hydrogen bonds : bond 0.16498 ( 856) hydrogen bonds : angle 9.32366 ( 2448) covalent geometry : bond 0.00839 (33792) covalent geometry : angle 1.04624 (46104) *********************** 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 : 3.422 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: A 10 VAL cc_start: 0.8492 (t) cc_final: 0.8217 (m) REVERT: A 23 GLN cc_start: 0.7797 (pp30) cc_final: 0.7323 (pp30) REVERT: A 62 TRP cc_start: 0.8361 (t60) cc_final: 0.7815 (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: 0.7936 (mmm) REVERT: A 100 TYR cc_start: 0.7333 (t80) cc_final: 0.6545 (t80) REVERT: A 132 SER cc_start: 0.8826 (m) cc_final: 0.8149 (t) REVERT: A 144 ASP cc_start: 0.8066 (m-30) cc_final: 0.7773 (t0) REVERT: A 187 MET cc_start: 0.8317 (ttp) cc_final: 0.8108 (ttp) REVERT: A 233 ASP cc_start: 0.7744 (p0) cc_final: 0.7308 (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: 0.6523 (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: 0.8404 (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: 0.6930 (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: 0.8107 (tp) REVERT: A 672 VAL cc_start: 0.8506 (m) cc_final: 0.7999 (t) REVERT: A 677 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7895 (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: 0.6862 (tmmt) REVERT: A 777 LEU cc_start: 0.8044 (mt) cc_final: 0.7816 (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: 0.6630 (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: 0.6172 (tp) REVERT: A 925 MET cc_start: 0.8128 (mmm) cc_final: 0.7660 (mmt) REVERT: A 955 PHE cc_start: 0.8580 (p90) cc_final: 0.8232 (p90) REVERT: A 974 HIS cc_start: 0.7714 (p-80) cc_final: 0.7310 (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: 0.7796 (p) REVERT: B 18 ASN cc_start: 0.8742 (t0) cc_final: 0.8227 (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: 0.7784 (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: 0.8449 (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: 0.7832 (m-30) REVERT: B 161 TYR cc_start: 0.7853 (t80) cc_final: 0.7459 (t80) REVERT: B 187 MET cc_start: 0.8503 (ttp) cc_final: 0.8293 (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: 0.7393 (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: 0.8333 (m-40) REVERT: B 411 ASP cc_start: 0.7611 (t0) cc_final: 0.7370 (t70) REVERT: B 443 MET cc_start: 0.7874 (ttp) cc_final: 0.7592 (ttm) REVERT: B 487 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7465 (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: 0.7994 (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: 0.6494 (mmt) REVERT: B 625 GLN cc_start: 0.7833 (pt0) cc_final: 0.7576 (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: 0.7609 (t) REVERT: B 655 MET cc_start: 0.7795 (ttt) cc_final: 0.7514 (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: 0.8196 (t) REVERT: B 677 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8039 (mtpp) REVERT: B 693 GLN cc_start: 0.7005 (tp40) cc_final: 0.6682 (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: 0.7992 (p0) REVERT: B 837 THR cc_start: 0.7530 (p) cc_final: 0.7247 (t) REVERT: B 852 SER cc_start: 0.8687 (t) cc_final: 0.8376 (p) REVERT: B 853 ARG cc_start: 0.7403 (mtt90) cc_final: 0.6945 (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: 0.5775 (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: 0.7233 (p-80) REVERT: B 975 LEU cc_start: 0.8633 (mt) cc_final: 0.8239 (mt) REVERT: B 1016 TYR cc_start: 0.7870 (p90) cc_final: 0.7663 (p90) REVERT: B 1019 VAL cc_start: 0.8391 (t) cc_final: 0.7903 (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: 0.7880 (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: 0.8554 (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: 0.7594 (t0) REVERT: C 161 TYR cc_start: 0.7921 (t80) cc_final: 0.7432 (t80) REVERT: C 187 MET cc_start: 0.8367 (ttp) cc_final: 0.8107 (ttp) REVERT: C 233 ASP cc_start: 0.7747 (p0) cc_final: 0.7355 (p0) REVERT: C 288 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7203 (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: 0.7439 (ttm) REVERT: C 461 GLU cc_start: 0.7284 (mm-30) cc_final: 0.7076 (mt-10) REVERT: C 492 ASP cc_start: 0.7771 (t0) cc_final: 0.7426 (t0) REVERT: C 515 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8188 (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: 0.7827 (t) REVERT: C 655 MET cc_start: 0.7865 (ttt) cc_final: 0.7630 (ttm) REVERT: C 670 LEU cc_start: 0.8192 (tt) cc_final: 0.7898 (tp) REVERT: C 672 VAL cc_start: 0.8601 (m) cc_final: 0.8183 (t) REVERT: C 677 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7943 (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: 0.7888 (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: 0.6994 (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: 0.7503 (t) REVERT: C 853 ARG cc_start: 0.7629 (mtt90) cc_final: 0.7196 (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: 0.7995 (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: 0.8200 (p90) REVERT: C 974 HIS cc_start: 0.7674 (p-80) cc_final: 0.7316 (p-80) REVERT: C 975 LEU cc_start: 0.8557 (mt) cc_final: 0.8030 (mt) REVERT: C 1019 VAL cc_start: 0.8363 (t) cc_final: 0.7867 (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: 0.7660 (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: 0.8000 (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: 0.6750 (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: 0.6585 (pp20) REVERT: D 255 ARG cc_start: 0.7693 (mmt90) cc_final: 0.7414 (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: 0.8112 (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: 0.7599 (ttm) REVERT: D 670 LEU cc_start: 0.8293 (tt) cc_final: 0.8015 (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: 0.7985 (mtpt) REVERT: D 693 GLN cc_start: 0.7043 (tp40) cc_final: 0.6757 (tp40) REVERT: D 699 ARG cc_start: 0.7034 (ptp-110) cc_final: 0.6795 (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: 0.7886 (p) REVERT: D 773 LYS cc_start: 0.7020 (tmmt) cc_final: 0.6788 (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: 0.6418 (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: 0.6669 (t70) REVERT: D 853 ARG cc_start: 0.7810 (mtt90) cc_final: 0.7402 (mtt90) REVERT: D 898 LEU cc_start: 0.7014 (tp) cc_final: 0.6210 (tp) REVERT: D 924 ASP cc_start: 0.8357 (m-30) cc_final: 0.7802 (t0) REVERT: D 925 MET cc_start: 0.8127 (mmm) cc_final: 0.7849 (mmt) REVERT: D 997 ASP cc_start: 0.7561 (m-30) cc_final: 0.7325 (m-30) REVERT: D 1007 PHE cc_start: 0.8401 (m-10) cc_final: 0.8008 (m-10) REVERT: D 1016 TYR cc_start: 0.7884 (p90) cc_final: 0.7609 (p90) REVERT: D 1019 VAL cc_start: 0.8441 (t) cc_final: 0.7976 (p) outliers start: 12 outliers final: 2 residues processed: 1058 average time/residue: 0.4729 time to fit residues: 772.3877 Evaluate side-chains 863 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 859 time to evaluate : 3.583 ------------------------------------------------------------------------------- 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 344 optimal weight: 0.8980 chunk 309 optimal weight: 0.0980 chunk 171 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 319 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 238 optimal weight: 0.6980 chunk 370 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 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 468 HIS ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 ASN B 628 GLN B 775 GLN B 844 HIS B 990 HIS C 25 ASN C 30 HIS C 155 ASN C 163 GLN C 382 ASN C 468 HIS C 540 HIS C 604 ASN C 628 GLN C 725 ASN C 775 GLN ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN D 30 HIS D 155 ASN D 163 GLN D 382 ASN D 604 ASN D 628 GLN D 719 GLN D 775 GLN ** D 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.099454 restraints weight = 56934.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.102835 restraints weight = 26796.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.105055 restraints weight = 15413.483| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33792 Z= 0.120 Angle : 0.645 7.958 46104 Z= 0.337 Chirality : 0.045 0.175 4820 Planarity : 0.005 0.046 6088 Dihedral : 5.472 38.359 4478 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.29 % Allowed : 10.53 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.12), residues: 4080 helix: -3.54 (0.19), residues: 356 sheet: -0.36 (0.14), residues: 1360 loop : -2.63 (0.11), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 568 HIS 0.010 0.001 HIS D 974 PHE 0.014 0.001 PHE D 764 TYR 0.018 0.001 TYR A 161 ARG 0.008 0.001 ARG B 630 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 856) hydrogen bonds : angle 6.37160 ( 2448) covalent geometry : bond 0.00264 (33792) covalent geometry : angle 0.64505 (46104) *********************** 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 942 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 862 time to evaluate : 3.477 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: A 46 ARG cc_start: 0.8399 (ttm110) cc_final: 0.7839 (ttm110) REVERT: A 62 TRP cc_start: 0.7990 (t60) cc_final: 0.7531 (t60) REVERT: A 67 GLU cc_start: 0.7589 (mp0) cc_final: 0.7321 (mp0) REVERT: A 75 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 84 VAL cc_start: 0.8010 (t) cc_final: 0.7454 (p) REVERT: A 85 VAL cc_start: 0.8731 (t) cc_final: 0.8484 (p) REVERT: A 92 MET cc_start: 0.8298 (mmm) cc_final: 0.7860 (mmm) REVERT: A 100 TYR cc_start: 0.6848 (t80) cc_final: 0.6146 (t80) REVERT: A 144 ASP cc_start: 0.7927 (m-30) cc_final: 0.7334 (m-30) REVERT: A 161 TYR cc_start: 0.7838 (t80) cc_final: 0.7501 (t80) REVERT: A 187 MET cc_start: 0.8302 (ttp) cc_final: 0.8085 (ttp) REVERT: A 233 ASP cc_start: 0.7547 (p0) cc_final: 0.7225 (p0) REVERT: A 243 GLU cc_start: 0.7142 (tt0) cc_final: 0.6770 (tt0) REVERT: A 338 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7178 (tm-30) REVERT: A 403 ASP cc_start: 0.7327 (m-30) cc_final: 0.6849 (m-30) REVERT: A 487 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7722 (tm-30) REVERT: A 492 ASP cc_start: 0.7637 (t0) cc_final: 0.7102 (t0) REVERT: A 515 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8169 (m) REVERT: A 518 TRP cc_start: 0.8485 (m100) cc_final: 0.8081 (m100) REVERT: A 585 TRP cc_start: 0.8732 (p-90) cc_final: 0.8008 (p-90) REVERT: A 599 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.5243 (pmt-80) REVERT: A 634 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8303 (mm-40) REVERT: A 637 GLU cc_start: 0.7092 (tt0) cc_final: 0.6632 (tt0) REVERT: A 655 MET cc_start: 0.7934 (ttt) cc_final: 0.7658 (ttm) REVERT: A 677 LYS cc_start: 0.8265 (mtpt) cc_final: 0.7763 (mtpt) REVERT: A 693 GLN cc_start: 0.6936 (tp40) cc_final: 0.6733 (tp40) REVERT: A 709 SER cc_start: 0.8254 (t) cc_final: 0.7770 (p) REVERT: A 748 CYS cc_start: 0.8486 (m) cc_final: 0.8209 (m) REVERT: A 773 LYS cc_start: 0.7193 (tmmt) cc_final: 0.6903 (tmmt) REVERT: A 777 LEU cc_start: 0.7906 (mt) cc_final: 0.7695 (mp) REVERT: A 792 ASP cc_start: 0.7853 (p0) cc_final: 0.7575 (p0) REVERT: A 853 ARG cc_start: 0.7299 (mtt90) cc_final: 0.7079 (mtt90) REVERT: A 935 ASN cc_start: 0.8963 (p0) cc_final: 0.8743 (p0) REVERT: A 955 PHE cc_start: 0.8373 (p90) cc_final: 0.7820 (p90) REVERT: A 974 HIS cc_start: 0.7663 (p-80) cc_final: 0.7274 (p-80) REVERT: A 975 LEU cc_start: 0.8602 (mt) cc_final: 0.8079 (mt) REVERT: A 997 ASP cc_start: 0.7324 (m-30) cc_final: 0.7092 (t0) REVERT: A 1016 TYR cc_start: 0.7377 (p90) cc_final: 0.6616 (p90) REVERT: B 9 VAL cc_start: 0.9252 (m) cc_final: 0.8975 (p) REVERT: B 37 ARG cc_start: 0.7721 (ttm170) cc_final: 0.7502 (tpp-160) REVERT: B 62 TRP cc_start: 0.8004 (t60) cc_final: 0.7633 (t60) REVERT: B 67 GLU cc_start: 0.7557 (mp0) cc_final: 0.7309 (mp0) REVERT: B 84 VAL cc_start: 0.8180 (t) cc_final: 0.7628 (p) REVERT: B 85 VAL cc_start: 0.8677 (t) cc_final: 0.8405 (p) REVERT: B 92 MET cc_start: 0.8476 (mmm) cc_final: 0.7991 (mmm) REVERT: B 100 TYR cc_start: 0.6897 (t80) cc_final: 0.6399 (t80) REVERT: B 144 ASP cc_start: 0.8158 (m-30) cc_final: 0.7617 (m-30) REVERT: B 187 MET cc_start: 0.8489 (ttp) cc_final: 0.8214 (ttp) REVERT: B 202 MET cc_start: 0.7762 (ptt) cc_final: 0.7554 (ptm) REVERT: B 211 ASP cc_start: 0.7630 (t0) cc_final: 0.7385 (t0) REVERT: B 237 ARG cc_start: 0.7303 (mtp85) cc_final: 0.6470 (mtp85) REVERT: B 288 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7417 (mtt-85) REVERT: B 403 ASP cc_start: 0.7350 (m-30) cc_final: 0.6855 (m-30) REVERT: B 411 ASP cc_start: 0.7414 (t0) cc_final: 0.7020 (m-30) REVERT: B 492 ASP cc_start: 0.7652 (t0) cc_final: 0.7175 (t0) REVERT: B 518 TRP cc_start: 0.8578 (m100) cc_final: 0.8138 (m100) REVERT: B 544 ASN cc_start: 0.8574 (m-40) cc_final: 0.8251 (m-40) REVERT: B 570 TRP cc_start: 0.7733 (t-100) cc_final: 0.7245 (t-100) REVERT: B 585 TRP cc_start: 0.8597 (p-90) cc_final: 0.7602 (p-90) REVERT: B 599 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.5293 (pmt-80) REVERT: B 603 MET cc_start: 0.6758 (mmt) cc_final: 0.6392 (mmt) REVERT: B 625 GLN cc_start: 0.7741 (pt0) cc_final: 0.7509 (pt0) REVERT: B 634 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8501 (mm110) REVERT: B 637 GLU cc_start: 0.7183 (tt0) cc_final: 0.6809 (tt0) REVERT: B 655 MET cc_start: 0.7804 (ttt) cc_final: 0.7552 (ttm) REVERT: B 667 GLU cc_start: 0.7208 (pm20) cc_final: 0.6717 (pm20) REVERT: B 672 VAL cc_start: 0.8485 (m) cc_final: 0.8104 (t) REVERT: B 677 LYS cc_start: 0.8458 (mtpt) cc_final: 0.7852 (mtpp) REVERT: B 693 GLN cc_start: 0.6972 (tp40) cc_final: 0.5665 (tp40) REVERT: B 708 TRP cc_start: 0.8233 (p-90) cc_final: 0.7874 (p-90) REVERT: B 721 ARG cc_start: 0.7352 (mtp180) cc_final: 0.7117 (mtp-110) REVERT: B 748 CYS cc_start: 0.8422 (m) cc_final: 0.8178 (m) REVERT: B 749 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7056 (tp) REVERT: B 756 TRP cc_start: 0.7341 (m-90) cc_final: 0.7139 (m-90) REVERT: B 808 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7419 (mm-30) REVERT: B 906 TYR cc_start: 0.7309 (m-10) cc_final: 0.6889 (m-10) REVERT: B 919 ASP cc_start: 0.8054 (m-30) cc_final: 0.7707 (t0) REVERT: B 955 PHE cc_start: 0.8250 (p90) cc_final: 0.8005 (p90) REVERT: B 997 ASP cc_start: 0.7347 (m-30) cc_final: 0.7011 (t0) REVERT: B 1016 TYR cc_start: 0.7161 (p90) cc_final: 0.6954 (p90) REVERT: B 1018 LEU cc_start: 0.8572 (pp) cc_final: 0.8353 (mt) REVERT: C 9 VAL cc_start: 0.9185 (m) cc_final: 0.8936 (p) REVERT: C 46 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7941 (ttm110) REVERT: C 62 TRP cc_start: 0.8165 (t60) cc_final: 0.7751 (t60) REVERT: C 84 VAL cc_start: 0.8200 (t) cc_final: 0.7694 (p) REVERT: C 85 VAL cc_start: 0.8831 (t) cc_final: 0.8574 (p) REVERT: C 92 MET cc_start: 0.8321 (mmm) cc_final: 0.7873 (mmm) REVERT: C 100 TYR cc_start: 0.7162 (t80) cc_final: 0.6304 (t80) REVERT: C 144 ASP cc_start: 0.8023 (m-30) cc_final: 0.7473 (m-30) REVERT: C 187 MET cc_start: 0.8364 (ttp) cc_final: 0.8037 (ttp) REVERT: C 211 ASP cc_start: 0.7921 (t0) cc_final: 0.7658 (m-30) REVERT: C 221 GLN cc_start: 0.8266 (pm20) cc_final: 0.7812 (pm20) REVERT: C 233 ASP cc_start: 0.7555 (p0) cc_final: 0.7303 (p0) REVERT: C 237 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.7217 (mtp85) REVERT: C 246 MET cc_start: 0.8193 (ppp) cc_final: 0.7954 (tmm) REVERT: C 343 LEU cc_start: 0.8048 (mt) cc_final: 0.7841 (mt) REVERT: C 349 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7465 (tp) REVERT: C 403 ASP cc_start: 0.7189 (m-30) cc_final: 0.6603 (m-30) REVERT: C 444 VAL cc_start: 0.7871 (t) cc_final: 0.7665 (p) REVERT: C 461 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7130 (mt-10) REVERT: C 492 ASP cc_start: 0.7624 (t0) cc_final: 0.7218 (t0) REVERT: C 515 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.7929 (m) REVERT: C 518 TRP cc_start: 0.8393 (m100) cc_final: 0.7908 (m100) REVERT: C 585 TRP cc_start: 0.8645 (p-90) cc_final: 0.8062 (p-90) REVERT: C 599 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.5240 (pmt-80) REVERT: C 603 MET cc_start: 0.6743 (mmt) cc_final: 0.6480 (mmt) REVERT: C 634 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8447 (mm-40) REVERT: C 637 GLU cc_start: 0.6988 (tt0) cc_final: 0.6564 (tt0) REVERT: C 677 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7785 (mtpt) REVERT: C 687 GLN cc_start: 0.7857 (pt0) cc_final: 0.7596 (pm20) REVERT: C 693 GLN cc_start: 0.7042 (tp40) cc_final: 0.6839 (tp40) REVERT: C 739 HIS cc_start: 0.7204 (t70) cc_final: 0.6954 (t70) REVERT: C 773 LYS cc_start: 0.7116 (tmmt) cc_final: 0.6808 (tmmt) REVERT: C 792 ASP cc_start: 0.8000 (p0) cc_final: 0.7702 (p0) REVERT: C 808 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7535 (mm-30) REVERT: C 853 ARG cc_start: 0.7756 (mtt90) cc_final: 0.7470 (mtt90) REVERT: C 857 ARG cc_start: 0.7727 (tpt-90) cc_final: 0.7489 (tpt-90) REVERT: C 924 ASP cc_start: 0.8398 (m-30) cc_final: 0.8025 (t0) REVERT: C 942 ARG cc_start: 0.8240 (mmm-85) cc_final: 0.7977 (tpp80) REVERT: C 955 PHE cc_start: 0.8360 (p90) cc_final: 0.8007 (p90) REVERT: C 997 ASP cc_start: 0.7418 (m-30) cc_final: 0.6931 (t0) REVERT: D 10 VAL cc_start: 0.8327 (t) cc_final: 0.7974 (m) REVERT: D 62 TRP cc_start: 0.7948 (t60) cc_final: 0.7629 (t60) REVERT: D 67 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7381 (mp0) REVERT: D 75 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7552 (tm-30) REVERT: D 84 VAL cc_start: 0.8168 (t) cc_final: 0.7597 (p) REVERT: D 85 VAL cc_start: 0.8679 (t) cc_final: 0.8428 (p) REVERT: D 92 MET cc_start: 0.8476 (mmm) cc_final: 0.7985 (mmm) REVERT: D 100 TYR cc_start: 0.7138 (t80) cc_final: 0.6719 (t80) REVERT: D 144 ASP cc_start: 0.8108 (m-30) cc_final: 0.7584 (m-30) REVERT: D 163 GLN cc_start: 0.7189 (tp-100) cc_final: 0.6944 (tp40) REVERT: D 187 MET cc_start: 0.8502 (ttp) cc_final: 0.8177 (ttp) REVERT: D 202 MET cc_start: 0.7750 (ptt) cc_final: 0.7547 (ptp) REVERT: D 237 ARG cc_start: 0.7471 (mtp85) cc_final: 0.7237 (mtp85) REVERT: D 243 GLU cc_start: 0.6907 (tt0) cc_final: 0.6549 (tt0) REVERT: D 288 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7530 (mtt-85) REVERT: D 403 ASP cc_start: 0.7508 (m-30) cc_final: 0.7131 (m-30) REVERT: D 444 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8259 (t) REVERT: D 492 ASP cc_start: 0.7585 (t0) cc_final: 0.7192 (t0) REVERT: D 518 TRP cc_start: 0.8502 (m100) cc_final: 0.8045 (m100) REVERT: D 585 TRP cc_start: 0.8546 (p-90) cc_final: 0.7884 (p-90) REVERT: D 599 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.5335 (ptt-90) REVERT: D 603 MET cc_start: 0.6662 (mmt) cc_final: 0.6204 (mmt) REVERT: D 625 GLN cc_start: 0.7504 (pt0) cc_final: 0.7200 (pt0) REVERT: D 634 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8496 (mm-40) REVERT: D 648 ASP cc_start: 0.7897 (t0) cc_final: 0.7678 (t0) REVERT: D 655 MET cc_start: 0.7810 (ttt) cc_final: 0.7583 (ttm) REVERT: D 672 VAL cc_start: 0.8635 (m) cc_final: 0.8300 (t) REVERT: D 677 LYS cc_start: 0.8403 (mtpt) cc_final: 0.7958 (mtpt) REVERT: D 693 GLN cc_start: 0.6965 (tp40) cc_final: 0.6613 (tp40) REVERT: D 699 ARG cc_start: 0.6803 (ptp-110) cc_final: 0.6552 (ptp-170) REVERT: D 709 SER cc_start: 0.8380 (t) cc_final: 0.7832 (p) REVERT: D 739 HIS cc_start: 0.6698 (t70) cc_final: 0.6334 (t-90) REVERT: D 749 ILE cc_start: 0.7345 (mt) cc_final: 0.6781 (tp) REVERT: D 756 TRP cc_start: 0.7865 (m-90) cc_final: 0.7251 (m-90) REVERT: D 924 ASP cc_start: 0.8297 (m-30) cc_final: 0.7877 (t0) REVERT: D 1016 TYR cc_start: 0.7379 (p90) cc_final: 0.7129 (p90) outliers start: 80 outliers final: 38 residues processed: 909 average time/residue: 0.4523 time to fit residues: 641.9040 Evaluate side-chains 849 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 802 time to evaluate : 3.255 ------------------------------------------------------------------------------- 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 362 LEU 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 749 ILE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 74 LEU 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 749 ILE Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 977 HIS 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 421 VAL 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 659 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 984 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 336 optimal weight: 5.9990 chunk 383 optimal weight: 0.0570 chunk 128 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 397 optimal weight: 7.9990 chunk 318 optimal weight: 8.9990 chunk 262 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 3.1704 ------------------------------------------------------------------------------- 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 216 HIS A 226 HIS A 840 HIS A 890 GLN B 216 HIS B 226 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 GLN B 840 HIS B 890 GLN B1017 GLN C 155 ASN C 226 HIS C 725 ASN C 761 GLN C 840 HIS ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN D 216 HIS D 226 HIS D 840 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.112992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.094826 restraints weight = 57933.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.098109 restraints weight = 27108.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100293 restraints weight = 15681.869| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 33792 Z= 0.256 Angle : 0.731 8.306 46104 Z= 0.386 Chirality : 0.049 0.196 4820 Planarity : 0.005 0.046 6088 Dihedral : 5.550 36.673 4478 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.20 % Allowed : 13.39 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.12), residues: 4080 helix: -2.89 (0.23), residues: 364 sheet: -0.22 (0.14), residues: 1392 loop : -2.64 (0.11), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1020 HIS 0.010 0.002 HIS C 622 PHE 0.020 0.002 PHE C 989 TYR 0.021 0.002 TYR B 538 ARG 0.010 0.001 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.05780 ( 856) hydrogen bonds : angle 5.99707 ( 2448) covalent geometry : bond 0.00592 (33792) covalent geometry : angle 0.73140 (46104) *********************** 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 952 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 840 time to evaluate : 3.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TRP cc_start: 0.8275 (t60) cc_final: 0.7783 (t60) REVERT: A 67 GLU cc_start: 0.7748 (mp0) cc_final: 0.7535 (mp0) REVERT: A 75 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 84 VAL cc_start: 0.8187 (t) cc_final: 0.7671 (p) REVERT: A 85 VAL cc_start: 0.8748 (t) cc_final: 0.8501 (p) REVERT: A 92 MET cc_start: 0.8311 (mmm) cc_final: 0.7856 (mmm) REVERT: A 100 TYR cc_start: 0.7297 (t80) cc_final: 0.6399 (t80) REVERT: A 144 ASP cc_start: 0.7990 (m-30) cc_final: 0.7618 (t0) REVERT: A 187 MET cc_start: 0.8312 (ttp) cc_final: 0.8060 (ttp) REVERT: A 237 ARG cc_start: 0.7349 (mtp85) cc_final: 0.7083 (mtp85) REVERT: A 243 GLU cc_start: 0.7137 (tt0) cc_final: 0.6791 (tt0) REVERT: A 338 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7141 (tm-30) REVERT: A 492 ASP cc_start: 0.7999 (t0) cc_final: 0.7557 (t0) REVERT: A 515 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8233 (m) REVERT: A 585 TRP cc_start: 0.8760 (p-90) cc_final: 0.7750 (p90) REVERT: A 599 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6774 (pmt-80) REVERT: A 634 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8492 (mm-40) REVERT: A 637 GLU cc_start: 0.7247 (tt0) cc_final: 0.6718 (tt0) REVERT: A 655 MET cc_start: 0.7904 (ttt) cc_final: 0.7625 (ttm) REVERT: A 677 LYS cc_start: 0.8296 (mtpt) cc_final: 0.7694 (mtpt) REVERT: A 682 LEU cc_start: 0.8580 (tp) cc_final: 0.8205 (tp) REVERT: A 693 GLN cc_start: 0.7084 (tp40) cc_final: 0.6707 (tp40) REVERT: A 773 LYS cc_start: 0.7278 (tmmt) cc_final: 0.6913 (tmmt) REVERT: A 792 ASP cc_start: 0.7828 (p0) cc_final: 0.7565 (p0) REVERT: A 924 ASP cc_start: 0.8301 (m-30) cc_final: 0.7983 (t0) REVERT: A 935 ASN cc_start: 0.8933 (p0) cc_final: 0.8604 (p0) REVERT: A 955 PHE cc_start: 0.8474 (p90) cc_final: 0.8024 (p90) REVERT: A 961 ARG cc_start: 0.7807 (tpt-90) cc_final: 0.7567 (ttt90) REVERT: A 973 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7952 (ptm160) REVERT: A 974 HIS cc_start: 0.7702 (p-80) cc_final: 0.6876 (p90) REVERT: A 975 LEU cc_start: 0.8647 (mt) cc_final: 0.8250 (mm) REVERT: A 1019 VAL cc_start: 0.8508 (t) cc_final: 0.8050 (p) REVERT: B 9 VAL cc_start: 0.9242 (m) cc_final: 0.8961 (p) REVERT: B 62 TRP cc_start: 0.8249 (t60) cc_final: 0.7547 (t60) REVERT: B 84 VAL cc_start: 0.8339 (t) cc_final: 0.7789 (p) REVERT: B 85 VAL cc_start: 0.8717 (t) cc_final: 0.8450 (p) REVERT: B 90 TRP cc_start: 0.7852 (p90) cc_final: 0.7240 (p90) REVERT: B 92 MET cc_start: 0.8510 (mmm) cc_final: 0.8017 (mmm) REVERT: B 100 TYR cc_start: 0.7387 (t80) cc_final: 0.6612 (t80) REVERT: B 144 ASP cc_start: 0.8160 (m-30) cc_final: 0.7632 (m-30) REVERT: B 161 TYR cc_start: 0.7675 (t80) cc_final: 0.7450 (t80) REVERT: B 211 ASP cc_start: 0.7635 (t0) cc_final: 0.7307 (t0) REVERT: B 237 ARG cc_start: 0.7356 (mtp85) cc_final: 0.6469 (mtp85) REVERT: B 245 GLN cc_start: 0.6932 (tp40) cc_final: 0.6674 (tt0) REVERT: B 288 ARG cc_start: 0.7963 (mtt-85) cc_final: 0.6640 (mtt-85) REVERT: B 299 LYS cc_start: 0.8175 (mmmm) cc_final: 0.7576 (mtpp) REVERT: B 338 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7454 (tm-30) REVERT: B 403 ASP cc_start: 0.7224 (m-30) cc_final: 0.6802 (m-30) REVERT: B 411 ASP cc_start: 0.7490 (t0) cc_final: 0.7060 (m-30) REVERT: B 412 GLU cc_start: 0.7339 (tt0) cc_final: 0.7019 (tt0) REVERT: B 492 ASP cc_start: 0.7965 (t0) cc_final: 0.7540 (t0) REVERT: B 544 ASN cc_start: 0.8496 (m-40) cc_final: 0.8205 (m-40) REVERT: B 570 TRP cc_start: 0.7698 (t-100) cc_final: 0.7339 (t-100) REVERT: B 599 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6630 (pmt-80) REVERT: B 603 MET cc_start: 0.7173 (mmt) cc_final: 0.6507 (mmt) REVERT: B 634 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8605 (mm110) REVERT: B 637 GLU cc_start: 0.7255 (tt0) cc_final: 0.6886 (tt0) REVERT: B 655 MET cc_start: 0.7913 (ttt) cc_final: 0.7630 (ttm) REVERT: B 667 GLU cc_start: 0.7250 (pm20) cc_final: 0.6670 (pm20) REVERT: B 672 VAL cc_start: 0.8442 (m) cc_final: 0.8219 (t) REVERT: B 677 LYS cc_start: 0.8491 (mtpt) cc_final: 0.7955 (mtpp) REVERT: B 693 GLN cc_start: 0.7062 (tp40) cc_final: 0.5770 (tp40) REVERT: B 708 TRP cc_start: 0.8224 (p-90) cc_final: 0.7809 (p-90) REVERT: B 721 ARG cc_start: 0.7466 (mtp180) cc_final: 0.7119 (mtp-110) REVERT: B 749 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7148 (tp) REVERT: B 756 TRP cc_start: 0.7581 (m-90) cc_final: 0.7064 (m-90) REVERT: B 905 ASN cc_start: 0.6968 (p0) cc_final: 0.6600 (p0) REVERT: B 906 TYR cc_start: 0.7458 (m-10) cc_final: 0.7130 (m-10) REVERT: B 919 ASP cc_start: 0.8005 (m-30) cc_final: 0.7603 (t0) REVERT: B 973 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8037 (ptm160) REVERT: B 975 LEU cc_start: 0.8627 (mt) cc_final: 0.8412 (mt) REVERT: B 983 TRP cc_start: 0.7969 (m100) cc_final: 0.7591 (m100) REVERT: B 997 ASP cc_start: 0.7399 (m-30) cc_final: 0.7066 (m-30) REVERT: B 1016 TYR cc_start: 0.7379 (p90) cc_final: 0.6940 (p90) REVERT: B 1019 VAL cc_start: 0.8532 (t) cc_final: 0.8070 (p) REVERT: C 9 VAL cc_start: 0.9184 (m) cc_final: 0.8929 (p) REVERT: C 15 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7876 (t0) REVERT: C 44 THR cc_start: 0.9016 (t) cc_final: 0.8685 (t) REVERT: C 46 ARG cc_start: 0.8266 (mtt180) cc_final: 0.8003 (ttm-80) REVERT: C 62 TRP cc_start: 0.8405 (t60) cc_final: 0.7803 (t60) REVERT: C 77 ASP cc_start: 0.7855 (m-30) cc_final: 0.7633 (m-30) REVERT: C 84 VAL cc_start: 0.8375 (t) cc_final: 0.7831 (p) REVERT: C 85 VAL cc_start: 0.8851 (t) cc_final: 0.8567 (p) REVERT: C 92 MET cc_start: 0.8342 (mmm) cc_final: 0.8014 (mmt) REVERT: C 100 TYR cc_start: 0.7569 (t80) cc_final: 0.6500 (t80) REVERT: C 144 ASP cc_start: 0.8116 (m-30) cc_final: 0.7531 (m-30) REVERT: C 167 LEU cc_start: 0.7549 (mm) cc_final: 0.7163 (mp) REVERT: C 187 MET cc_start: 0.8366 (ttp) cc_final: 0.8075 (ttp) REVERT: C 211 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: C 221 GLN cc_start: 0.8293 (pm20) cc_final: 0.7761 (pm20) REVERT: C 237 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.7293 (mtp85) REVERT: C 299 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7710 (mtpp) REVERT: C 349 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7606 (tp) REVERT: C 403 ASP cc_start: 0.7168 (m-30) cc_final: 0.6675 (m-30) REVERT: C 444 VAL cc_start: 0.7876 (t) cc_final: 0.7649 (p) REVERT: C 461 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7057 (mt-10) REVERT: C 492 ASP cc_start: 0.7921 (t0) cc_final: 0.7619 (t0) REVERT: C 515 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8096 (m) REVERT: C 585 TRP cc_start: 0.8619 (p-90) cc_final: 0.8090 (p-90) REVERT: C 599 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6369 (pmt-80) REVERT: C 603 MET cc_start: 0.6916 (mmt) cc_final: 0.6492 (mmt) REVERT: C 634 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8490 (mm-40) REVERT: C 637 GLU cc_start: 0.7052 (tt0) cc_final: 0.6536 (tt0) REVERT: C 677 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7758 (mtpt) REVERT: C 687 GLN cc_start: 0.7934 (pt0) cc_final: 0.7683 (pm20) REVERT: C 693 GLN cc_start: 0.7199 (tp40) cc_final: 0.6717 (tp40) REVERT: C 708 TRP cc_start: 0.8323 (p-90) cc_final: 0.7872 (p-90) REVERT: C 721 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.6708 (ttm-80) REVERT: C 739 HIS cc_start: 0.7253 (t70) cc_final: 0.6957 (t70) REVERT: C 792 ASP cc_start: 0.7905 (p0) cc_final: 0.7636 (p0) REVERT: C 808 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7599 (mm-30) REVERT: C 837 THR cc_start: 0.8306 (p) cc_final: 0.8024 (t) REVERT: C 924 ASP cc_start: 0.8416 (m-30) cc_final: 0.8120 (t0) REVERT: C 955 PHE cc_start: 0.8450 (p90) cc_final: 0.8166 (p90) REVERT: C 973 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7979 (ptm160) REVERT: C 1019 VAL cc_start: 0.8481 (t) cc_final: 0.7999 (p) REVERT: D 62 TRP cc_start: 0.8318 (t60) cc_final: 0.7753 (t60) REVERT: D 67 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7435 (mp0) REVERT: D 74 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7408 (mt) REVERT: D 75 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7358 (tm-30) REVERT: D 84 VAL cc_start: 0.8297 (t) cc_final: 0.7785 (p) REVERT: D 85 VAL cc_start: 0.8680 (t) cc_final: 0.8469 (p) REVERT: D 92 MET cc_start: 0.8393 (mmm) cc_final: 0.8059 (mmt) REVERT: D 100 TYR cc_start: 0.7317 (t80) cc_final: 0.6563 (t80) REVERT: D 131 GLU cc_start: 0.6852 (tp30) cc_final: 0.6622 (tp30) REVERT: D 144 ASP cc_start: 0.8174 (m-30) cc_final: 0.7555 (m-30) REVERT: D 163 GLN cc_start: 0.7255 (tp-100) cc_final: 0.7040 (tp40) REVERT: D 167 LEU cc_start: 0.7507 (mt) cc_final: 0.7232 (mp) REVERT: D 187 MET cc_start: 0.8483 (ttp) cc_final: 0.8195 (ttp) REVERT: D 211 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: D 237 ARG cc_start: 0.7445 (mtp85) cc_final: 0.7241 (mtp85) REVERT: D 243 GLU cc_start: 0.6931 (tt0) cc_final: 0.6594 (tt0) REVERT: D 403 ASP cc_start: 0.7425 (m-30) cc_final: 0.7154 (m-30) REVERT: D 492 ASP cc_start: 0.7837 (t0) cc_final: 0.7473 (t0) REVERT: D 553 TRP cc_start: 0.8320 (m100) cc_final: 0.8101 (m100) REVERT: D 577 LYS cc_start: 0.8598 (tttt) cc_final: 0.8162 (ttmt) REVERT: D 585 TRP cc_start: 0.8585 (p-90) cc_final: 0.7424 (p90) REVERT: D 599 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6630 (pmt-80) REVERT: D 603 MET cc_start: 0.7022 (mmt) cc_final: 0.6481 (mmt) REVERT: D 625 GLN cc_start: 0.7283 (pt0) cc_final: 0.7002 (pt0) REVERT: D 634 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8576 (mm-40) REVERT: D 655 MET cc_start: 0.7849 (ttt) cc_final: 0.7645 (ttm) REVERT: D 670 LEU cc_start: 0.8305 (tt) cc_final: 0.8063 (tp) REVERT: D 672 VAL cc_start: 0.8495 (m) cc_final: 0.8272 (t) REVERT: D 677 LYS cc_start: 0.8461 (mtpt) cc_final: 0.7786 (mtpp) REVERT: D 693 GLN cc_start: 0.7043 (tp40) cc_final: 0.6780 (tp40) REVERT: D 699 ARG cc_start: 0.6921 (ptp-110) cc_final: 0.6677 (ptp-170) REVERT: D 708 TRP cc_start: 0.8311 (p-90) cc_final: 0.7910 (p-90) REVERT: D 709 SER cc_start: 0.8352 (t) cc_final: 0.7784 (p) REVERT: D 739 HIS cc_start: 0.7100 (t70) cc_final: 0.6604 (t70) REVERT: D 744 GLU cc_start: 0.8229 (pm20) cc_final: 0.7748 (pm20) REVERT: D 749 ILE cc_start: 0.7356 (mt) cc_final: 0.7097 (tp) REVERT: D 756 TRP cc_start: 0.8213 (m-90) cc_final: 0.7142 (m100) REVERT: D 768 MET cc_start: 0.5990 (ttm) cc_final: 0.5252 (ttm) REVERT: D 924 ASP cc_start: 0.8285 (m-30) cc_final: 0.7998 (t0) REVERT: D 952 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7419 (ttm110) REVERT: D 973 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8092 (ptm160) REVERT: D 1019 VAL cc_start: 0.8611 (t) cc_final: 0.8143 (p) outliers start: 112 outliers final: 75 residues processed: 898 average time/residue: 0.4799 time to fit residues: 672.5283 Evaluate side-chains 890 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 799 time to evaluate : 3.520 ------------------------------------------------------------------------------- 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 308 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 667 GLU 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 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 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 132 SER Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 241 GLU 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 362 LEU Chi-restraints excluded: chain B residue 376 ILE 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 745 MET Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain B residue 761 GLN Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 973 ARG Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 74 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 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 829 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 966 GLN Chi-restraints excluded: chain C residue 973 ARG 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 266 GLN Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 421 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 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 793 ILE Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 843 GLN Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 973 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 165 optimal weight: 2.9990 chunk 236 optimal weight: 8.9990 chunk 118 optimal weight: 0.0870 chunk 97 optimal weight: 9.9990 chunk 328 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 304 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- 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 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 HIS B 118 ASN B 155 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 HIS C 118 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 GLN C 840 HIS ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096874 restraints weight = 57375.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100226 restraints weight = 26802.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102421 restraints weight = 15411.178| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33792 Z= 0.157 Angle : 0.649 7.976 46104 Z= 0.338 Chirality : 0.046 0.203 4820 Planarity : 0.004 0.043 6088 Dihedral : 5.217 39.075 4478 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.46 % Allowed : 14.39 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.12), residues: 4080 helix: -2.59 (0.25), residues: 364 sheet: -0.18 (0.14), residues: 1432 loop : -2.54 (0.11), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 842 HIS 0.009 0.001 HIS C 974 PHE 0.012 0.001 PHE C 549 TYR 0.019 0.002 TYR C 161 ARG 0.009 0.001 ARG D 356 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 856) hydrogen bonds : angle 5.57962 ( 2448) covalent geometry : bond 0.00360 (33792) covalent geometry : angle 0.64938 (46104) *********************** 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 936 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 815 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TRP cc_start: 0.8188 (t60) cc_final: 0.7601 (t60) REVERT: A 67 GLU cc_start: 0.7774 (mp0) cc_final: 0.7548 (mp0) REVERT: A 75 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7298 (tm-30) REVERT: A 84 VAL cc_start: 0.8197 (t) cc_final: 0.7669 (p) REVERT: A 85 VAL cc_start: 0.8744 (t) cc_final: 0.8496 (p) REVERT: A 92 MET cc_start: 0.8314 (mmm) cc_final: 0.7811 (mmm) REVERT: A 131 GLU cc_start: 0.7455 (tp30) cc_final: 0.7047 (tp30) REVERT: A 144 ASP cc_start: 0.7990 (m-30) cc_final: 0.7555 (t0) REVERT: A 187 MET cc_start: 0.8264 (ttp) cc_final: 0.8040 (ttp) REVERT: A 237 ARG cc_start: 0.7299 (mtp85) cc_final: 0.6297 (mtp85) REVERT: A 243 GLU cc_start: 0.7096 (tt0) cc_final: 0.6773 (tt0) REVERT: A 338 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7241 (tm-30) REVERT: A 492 ASP cc_start: 0.7943 (t0) cc_final: 0.7493 (t0) REVERT: A 515 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8107 (m) REVERT: A 585 TRP cc_start: 0.8774 (p-90) cc_final: 0.7606 (p-90) REVERT: A 599 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6635 (pmt-80) REVERT: A 634 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8464 (mm-40) REVERT: A 637 GLU cc_start: 0.7318 (tt0) cc_final: 0.6583 (tt0) REVERT: A 655 MET cc_start: 0.7886 (ttt) cc_final: 0.7607 (ttm) REVERT: A 677 LYS cc_start: 0.8265 (mtpt) cc_final: 0.7621 (mtpt) REVERT: A 693 GLN cc_start: 0.7234 (tp40) cc_final: 0.6937 (tp40) REVERT: A 773 LYS cc_start: 0.7262 (tmmt) cc_final: 0.6922 (tmmt) REVERT: A 792 ASP cc_start: 0.7803 (p0) cc_final: 0.7535 (p0) REVERT: A 924 ASP cc_start: 0.8283 (m-30) cc_final: 0.7835 (t0) REVERT: A 935 ASN cc_start: 0.8897 (p0) cc_final: 0.8617 (p0) REVERT: A 973 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7854 (ptm160) REVERT: A 974 HIS cc_start: 0.7689 (p-80) cc_final: 0.7238 (p-80) REVERT: A 975 LEU cc_start: 0.8641 (mt) cc_final: 0.8127 (mt) REVERT: A 997 ASP cc_start: 0.7200 (m-30) cc_final: 0.6932 (t0) REVERT: A 1016 TYR cc_start: 0.7342 (p90) cc_final: 0.7014 (p90) REVERT: A 1019 VAL cc_start: 0.8507 (t) cc_final: 0.8025 (p) REVERT: B 9 VAL cc_start: 0.9133 (m) cc_final: 0.8890 (p) REVERT: B 62 TRP cc_start: 0.8132 (t60) cc_final: 0.7495 (t60) REVERT: B 77 ASP cc_start: 0.7883 (m-30) cc_final: 0.7676 (m-30) REVERT: B 84 VAL cc_start: 0.8271 (t) cc_final: 0.7711 (p) REVERT: B 85 VAL cc_start: 0.8702 (t) cc_final: 0.8443 (p) REVERT: B 90 TRP cc_start: 0.7774 (p90) cc_final: 0.7173 (p90) REVERT: B 92 MET cc_start: 0.8448 (mmm) cc_final: 0.7966 (mmm) REVERT: B 100 TYR cc_start: 0.7277 (t80) cc_final: 0.6417 (t80) REVERT: B 144 ASP cc_start: 0.8141 (m-30) cc_final: 0.7596 (m-30) REVERT: B 211 ASP cc_start: 0.7606 (t0) cc_final: 0.7267 (t0) REVERT: B 237 ARG cc_start: 0.7334 (mtp85) cc_final: 0.6433 (mtp85) REVERT: B 338 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7419 (tm-30) REVERT: B 403 ASP cc_start: 0.7238 (m-30) cc_final: 0.6838 (m-30) REVERT: B 411 ASP cc_start: 0.7383 (t0) cc_final: 0.6977 (m-30) REVERT: B 412 GLU cc_start: 0.7228 (tt0) cc_final: 0.6937 (tt0) REVERT: B 492 ASP cc_start: 0.7928 (t0) cc_final: 0.7503 (t0) REVERT: B 544 ASN cc_start: 0.8490 (m-40) cc_final: 0.8181 (m-40) REVERT: B 585 TRP cc_start: 0.8587 (p-90) cc_final: 0.7579 (p-90) REVERT: B 599 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6450 (pmt-80) REVERT: B 603 MET cc_start: 0.6987 (mmt) cc_final: 0.6467 (mmt) REVERT: B 634 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8606 (mm110) REVERT: B 637 GLU cc_start: 0.7262 (tt0) cc_final: 0.6736 (tt0) REVERT: B 655 MET cc_start: 0.7868 (ttt) cc_final: 0.7571 (ttm) REVERT: B 677 LYS cc_start: 0.8465 (mtpt) cc_final: 0.7809 (mtpp) REVERT: B 693 GLN cc_start: 0.7029 (tp40) cc_final: 0.6616 (tp40) REVERT: B 708 TRP cc_start: 0.8235 (p-90) cc_final: 0.7784 (p-90) REVERT: B 744 GLU cc_start: 0.8637 (pm20) cc_final: 0.8399 (pm20) REVERT: B 749 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7305 (tp) REVERT: B 756 TRP cc_start: 0.7422 (m-90) cc_final: 0.7018 (m-90) REVERT: B 919 ASP cc_start: 0.8042 (m-30) cc_final: 0.7629 (t0) REVERT: B 955 PHE cc_start: 0.8368 (p90) cc_final: 0.7824 (p90) REVERT: B 973 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7925 (ptm160) REVERT: B 987 ASP cc_start: 0.7295 (m-30) cc_final: 0.7086 (m-30) REVERT: B 1016 TYR cc_start: 0.7222 (p90) cc_final: 0.6900 (p90) REVERT: B 1019 VAL cc_start: 0.8466 (t) cc_final: 0.7866 (p) REVERT: C 9 VAL cc_start: 0.9163 (m) cc_final: 0.8930 (p) REVERT: C 15 ASP cc_start: 0.8291 (m-30) cc_final: 0.7855 (t0) REVERT: C 46 ARG cc_start: 0.8244 (mtt180) cc_final: 0.8036 (tpp80) REVERT: C 62 TRP cc_start: 0.8259 (t60) cc_final: 0.7775 (t60) REVERT: C 77 ASP cc_start: 0.7804 (m-30) cc_final: 0.7578 (m-30) REVERT: C 84 VAL cc_start: 0.8306 (t) cc_final: 0.7803 (p) REVERT: C 85 VAL cc_start: 0.8825 (t) cc_final: 0.8560 (p) REVERT: C 92 MET cc_start: 0.8280 (mmm) cc_final: 0.7770 (mmm) REVERT: C 144 ASP cc_start: 0.8064 (m-30) cc_final: 0.7453 (m-30) REVERT: C 187 MET cc_start: 0.8346 (ttp) cc_final: 0.8066 (ttp) REVERT: C 193 ASP cc_start: 0.7782 (p0) cc_final: 0.7558 (p0) REVERT: C 211 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7448 (m-30) REVERT: C 221 GLN cc_start: 0.8282 (pm20) cc_final: 0.7702 (pm20) REVERT: C 237 ARG cc_start: 0.7529 (ttm-80) cc_final: 0.7225 (mtp85) REVERT: C 299 LYS cc_start: 0.8205 (mmmm) cc_final: 0.7839 (mttp) REVERT: C 334 GLU cc_start: 0.6822 (tm-30) cc_final: 0.6601 (tm-30) REVERT: C 349 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7548 (tp) REVERT: C 403 ASP cc_start: 0.7176 (m-30) cc_final: 0.6631 (m-30) REVERT: C 444 VAL cc_start: 0.7837 (t) cc_final: 0.7620 (p) REVERT: C 492 ASP cc_start: 0.7890 (t0) cc_final: 0.7565 (t0) REVERT: C 515 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8017 (m) REVERT: C 585 TRP cc_start: 0.8623 (p-90) cc_final: 0.8150 (p-90) REVERT: C 599 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6311 (pmt-80) REVERT: C 603 MET cc_start: 0.6750 (mmt) cc_final: 0.6499 (mmt) REVERT: C 634 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8487 (mm-40) REVERT: C 637 GLU cc_start: 0.7096 (tt0) cc_final: 0.6423 (tt0) REVERT: C 677 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7653 (mtpt) REVERT: C 682 LEU cc_start: 0.8592 (tp) cc_final: 0.8341 (tp) REVERT: C 687 GLN cc_start: 0.7971 (pt0) cc_final: 0.7741 (pm20) REVERT: C 708 TRP cc_start: 0.8331 (p-90) cc_final: 0.7860 (p-90) REVERT: C 739 HIS cc_start: 0.7366 (t70) cc_final: 0.7132 (t70) REVERT: C 792 ASP cc_start: 0.7856 (p0) cc_final: 0.7585 (p0) REVERT: C 808 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7533 (mm-30) REVERT: C 924 ASP cc_start: 0.8410 (m-30) cc_final: 0.8066 (t0) REVERT: C 945 ASN cc_start: 0.7872 (m-40) cc_final: 0.7512 (t0) REVERT: C 955 PHE cc_start: 0.8435 (p90) cc_final: 0.7984 (p90) REVERT: C 973 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7986 (ptm160) REVERT: C 997 ASP cc_start: 0.7099 (m-30) cc_final: 0.6815 (t0) REVERT: C 1019 VAL cc_start: 0.8452 (t) cc_final: 0.7956 (p) REVERT: D 15 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7803 (t0) REVERT: D 62 TRP cc_start: 0.8200 (t60) cc_final: 0.7684 (t60) REVERT: D 67 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7472 (mp0) REVERT: D 75 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7455 (tm-30) REVERT: D 84 VAL cc_start: 0.8216 (t) cc_final: 0.7707 (p) REVERT: D 85 VAL cc_start: 0.8710 (t) cc_final: 0.8493 (p) REVERT: D 92 MET cc_start: 0.8346 (mmm) cc_final: 0.7999 (mmt) REVERT: D 100 TYR cc_start: 0.7186 (t80) cc_final: 0.6327 (t80) REVERT: D 131 GLU cc_start: 0.6912 (tp30) cc_final: 0.6571 (tp30) REVERT: D 144 ASP cc_start: 0.8155 (m-30) cc_final: 0.7514 (m-30) REVERT: D 187 MET cc_start: 0.8466 (ttp) cc_final: 0.8229 (ttp) REVERT: D 211 ASP cc_start: 0.7804 (t0) cc_final: 0.7406 (m-30) REVERT: D 243 GLU cc_start: 0.6943 (tt0) cc_final: 0.6571 (tt0) REVERT: D 245 GLN cc_start: 0.7314 (tt0) cc_final: 0.6479 (tt0) REVERT: D 288 ARG cc_start: 0.7770 (mtt180) cc_final: 0.7064 (mtt-85) REVERT: D 403 ASP cc_start: 0.7431 (m-30) cc_final: 0.7134 (m-30) REVERT: D 492 ASP cc_start: 0.7819 (t0) cc_final: 0.7440 (t0) REVERT: D 515 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7768 (m) REVERT: D 585 TRP cc_start: 0.8601 (p-90) cc_final: 0.7954 (p-90) REVERT: D 599 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6464 (pmt-80) REVERT: D 603 MET cc_start: 0.6689 (mmt) cc_final: 0.6153 (mmt) REVERT: D 634 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8553 (mm-40) REVERT: D 655 MET cc_start: 0.7820 (ttt) cc_final: 0.7584 (ttm) REVERT: D 670 LEU cc_start: 0.8237 (tt) cc_final: 0.8001 (tp) REVERT: D 672 VAL cc_start: 0.8446 (m) cc_final: 0.8246 (t) REVERT: D 677 LYS cc_start: 0.8410 (mtpt) cc_final: 0.7751 (mtpp) REVERT: D 693 GLN cc_start: 0.7199 (tp40) cc_final: 0.6692 (tp40) REVERT: D 699 ARG cc_start: 0.6795 (ptp-110) cc_final: 0.6557 (ptp-170) REVERT: D 708 TRP cc_start: 0.8326 (p-90) cc_final: 0.7894 (p-90) REVERT: D 709 SER cc_start: 0.8269 (t) cc_final: 0.7692 (p) REVERT: D 721 ARG cc_start: 0.7828 (ttm110) cc_final: 0.7614 (ttm-80) REVERT: D 739 HIS cc_start: 0.6949 (t70) cc_final: 0.6535 (t70) REVERT: D 768 MET cc_start: 0.5848 (ttm) cc_final: 0.5454 (ttm) REVERT: D 906 TYR cc_start: 0.7231 (m-10) cc_final: 0.7020 (m-10) REVERT: D 924 ASP cc_start: 0.8237 (m-30) cc_final: 0.7949 (t0) REVERT: D 952 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.7338 (ttm110) REVERT: D 973 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.8006 (ptm160) REVERT: D 997 ASP cc_start: 0.7320 (m-30) cc_final: 0.6740 (t0) REVERT: D 1019 VAL cc_start: 0.8608 (t) cc_final: 0.8128 (p) outliers start: 121 outliers final: 71 residues processed: 883 average time/residue: 0.4698 time to fit residues: 649.6204 Evaluate side-chains 880 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 794 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 494 THR 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 667 GLU 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 B residue 14 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 241 GLU 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 749 ILE Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 973 ARG Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 233 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 829 THR Chi-restraints excluded: chain C residue 871 GLU Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 973 ARG Chi-restraints excluded: chain C residue 977 HIS 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 86 VAL Chi-restraints excluded: chain D residue 230 ARG 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 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 884 LEU Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 973 ARG Chi-restraints excluded: chain D residue 977 HIS 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 337 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 239 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 chunk 294 optimal weight: 0.0570 chunk 1 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 chunk 152 optimal weight: 0.6980 chunk 264 optimal weight: 5.9990 chunk 403 optimal weight: 8.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 HIS A 890 GLN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 HIS C 359 HIS ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 840 HIS ** C 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099126 restraints weight = 57157.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102546 restraints weight = 26722.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.104802 restraints weight = 15322.448| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33792 Z= 0.099 Angle : 0.594 7.787 46104 Z= 0.304 Chirality : 0.044 0.273 4820 Planarity : 0.004 0.039 6088 Dihedral : 4.741 39.435 4478 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.29 % Allowed : 15.22 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 4080 helix: -2.04 (0.28), residues: 340 sheet: 0.09 (0.14), residues: 1432 loop : -2.33 (0.12), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 842 HIS 0.008 0.001 HIS C 974 PHE 0.011 0.001 PHE C 150 TYR 0.019 0.001 TYR C 161 ARG 0.006 0.000 ARG D 46 Details of bonding type rmsd hydrogen bonds : bond 0.03108 ( 856) hydrogen bonds : angle 5.11057 ( 2448) covalent geometry : bond 0.00218 (33792) covalent geometry : angle 0.59434 (46104) *********************** 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 937 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 822 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7454 (ttm-80) REVERT: A 46 ARG cc_start: 0.8244 (tpp80) cc_final: 0.8039 (ttm-80) REVERT: A 62 TRP cc_start: 0.8009 (t60) cc_final: 0.7488 (t60) REVERT: A 67 GLU cc_start: 0.7780 (mp0) cc_final: 0.7551 (mp0) REVERT: A 75 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7250 (tm-30) REVERT: A 84 VAL cc_start: 0.8082 (t) cc_final: 0.7513 (p) REVERT: A 85 VAL cc_start: 0.8715 (t) cc_final: 0.8446 (p) REVERT: A 92 MET cc_start: 0.8261 (mmm) cc_final: 0.7759 (mmm) REVERT: A 131 GLU cc_start: 0.7272 (tp30) cc_final: 0.6888 (tp30) REVERT: A 136 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7850 (mp0) REVERT: A 144 ASP cc_start: 0.7965 (m-30) cc_final: 0.7328 (m-30) REVERT: A 187 MET cc_start: 0.8251 (ttp) cc_final: 0.8001 (ttp) REVERT: A 221 GLN cc_start: 0.8116 (pm20) cc_final: 0.7897 (pm20) REVERT: A 233 ASP cc_start: 0.7845 (p0) cc_final: 0.7639 (p0) REVERT: A 243 GLU cc_start: 0.7029 (tt0) cc_final: 0.6791 (tt0) REVERT: A 288 ARG cc_start: 0.8000 (mtt-85) cc_final: 0.7449 (mtt-85) REVERT: A 338 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 473 ARG cc_start: 0.7966 (mmm160) cc_final: 0.7746 (tpt170) REVERT: A 492 ASP cc_start: 0.7833 (t0) cc_final: 0.7333 (t0) REVERT: A 494 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7963 (p) REVERT: A 585 TRP cc_start: 0.8761 (p-90) cc_final: 0.7964 (p-90) REVERT: A 599 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6451 (pmt-80) REVERT: A 634 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8421 (mm-40) REVERT: A 637 GLU cc_start: 0.7357 (tt0) cc_final: 0.6523 (tt0) REVERT: A 655 MET cc_start: 0.7877 (ttt) cc_final: 0.7590 (ttm) REVERT: A 677 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7510 (mtpt) REVERT: A 739 HIS cc_start: 0.7421 (t-90) cc_final: 0.7089 (t-90) REVERT: A 756 TRP cc_start: 0.7474 (m-90) cc_final: 0.7014 (m-90) REVERT: A 761 GLN cc_start: 0.7207 (mp10) cc_final: 0.7002 (mp10) REVERT: A 773 LYS cc_start: 0.7025 (tmmt) cc_final: 0.6790 (tmmt) REVERT: A 792 ASP cc_start: 0.7818 (p0) cc_final: 0.7538 (p0) REVERT: A 935 ASN cc_start: 0.8823 (p0) cc_final: 0.8568 (p0) REVERT: A 945 ASN cc_start: 0.7382 (m-40) cc_final: 0.7118 (t0) REVERT: A 955 PHE cc_start: 0.8313 (p90) cc_final: 0.8053 (p90) REVERT: A 973 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7644 (ptm160) REVERT: A 974 HIS cc_start: 0.7662 (p-80) cc_final: 0.7222 (p-80) REVERT: A 975 LEU cc_start: 0.8610 (mt) cc_final: 0.8158 (mt) REVERT: A 1016 TYR cc_start: 0.7177 (p90) cc_final: 0.6887 (p90) REVERT: B 9 VAL cc_start: 0.9091 (m) cc_final: 0.8872 (p) REVERT: B 43 ARG cc_start: 0.8401 (mtm110) cc_final: 0.7625 (ttm-80) REVERT: B 62 TRP cc_start: 0.7928 (t60) cc_final: 0.7412 (t60) REVERT: B 67 GLU cc_start: 0.7681 (mp0) cc_final: 0.7346 (mp0) REVERT: B 84 VAL cc_start: 0.8175 (t) cc_final: 0.7609 (p) REVERT: B 85 VAL cc_start: 0.8663 (t) cc_final: 0.8398 (p) REVERT: B 92 MET cc_start: 0.8465 (mmm) cc_final: 0.7994 (mmm) REVERT: B 136 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7845 (mp0) REVERT: B 144 ASP cc_start: 0.8137 (m-30) cc_final: 0.7570 (m-30) REVERT: B 211 ASP cc_start: 0.7560 (t0) cc_final: 0.7168 (t0) REVERT: B 237 ARG cc_start: 0.7301 (mtp85) cc_final: 0.6476 (mtp85) REVERT: B 299 LYS cc_start: 0.8105 (mmmm) cc_final: 0.7683 (mttp) REVERT: B 338 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7389 (tm-30) REVERT: B 403 ASP cc_start: 0.7251 (m-30) cc_final: 0.6849 (m-30) REVERT: B 411 ASP cc_start: 0.7307 (t0) cc_final: 0.6970 (m-30) REVERT: B 492 ASP cc_start: 0.7836 (t0) cc_final: 0.7334 (t0) REVERT: B 544 ASN cc_start: 0.8356 (m-40) cc_final: 0.8009 (m-40) REVERT: B 578 TYR cc_start: 0.8705 (m-10) cc_final: 0.8484 (m-10) REVERT: B 585 TRP cc_start: 0.8588 (p-90) cc_final: 0.7837 (p-90) REVERT: B 599 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.6100 (pmt-80) REVERT: B 634 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8490 (mm-40) REVERT: B 637 GLU cc_start: 0.7220 (tt0) cc_final: 0.6513 (tt0) REVERT: B 655 MET cc_start: 0.7821 (ttt) cc_final: 0.7542 (ttm) REVERT: B 677 LYS cc_start: 0.8413 (mtpt) cc_final: 0.7821 (mtpt) REVERT: B 693 GLN cc_start: 0.7003 (tp40) cc_final: 0.6758 (tp40) REVERT: B 708 TRP cc_start: 0.8291 (p-90) cc_final: 0.7809 (p-90) REVERT: B 749 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7282 (tp) REVERT: B 896 ASN cc_start: 0.7729 (t0) cc_final: 0.7464 (t0) REVERT: B 919 ASP cc_start: 0.8071 (m-30) cc_final: 0.7622 (t0) REVERT: B 955 PHE cc_start: 0.8304 (p90) cc_final: 0.8080 (p90) REVERT: B 973 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7803 (ptm160) REVERT: B 974 HIS cc_start: 0.7437 (p90) cc_final: 0.7115 (p90) REVERT: B 997 ASP cc_start: 0.7415 (m-30) cc_final: 0.6968 (t70) REVERT: B 1016 TYR cc_start: 0.7020 (p90) cc_final: 0.6734 (p90) REVERT: C 9 VAL cc_start: 0.9055 (m) cc_final: 0.8843 (p) REVERT: C 14 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7940 (mtp85) REVERT: C 15 ASP cc_start: 0.8096 (m-30) cc_final: 0.7663 (t0) REVERT: C 44 THR cc_start: 0.8985 (t) cc_final: 0.8498 (p) REVERT: C 46 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7930 (ttm-80) REVERT: C 62 TRP cc_start: 0.8095 (t60) cc_final: 0.7645 (t60) REVERT: C 84 VAL cc_start: 0.8145 (t) cc_final: 0.7623 (p) REVERT: C 85 VAL cc_start: 0.8767 (t) cc_final: 0.8478 (p) REVERT: C 92 MET cc_start: 0.8233 (mmm) cc_final: 0.7727 (mmm) REVERT: C 144 ASP cc_start: 0.8008 (m-30) cc_final: 0.7165 (m-30) REVERT: C 187 MET cc_start: 0.8306 (ttp) cc_final: 0.8007 (ttp) REVERT: C 211 ASP cc_start: 0.7772 (t0) cc_final: 0.7369 (m-30) REVERT: C 221 GLN cc_start: 0.8218 (pm20) cc_final: 0.7665 (pm20) REVERT: C 237 ARG cc_start: 0.7458 (ttm-80) cc_final: 0.7194 (mtp85) REVERT: C 349 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7464 (tp) REVERT: C 403 ASP cc_start: 0.7154 (m-30) cc_final: 0.6572 (m-30) REVERT: C 492 ASP cc_start: 0.7794 (t0) cc_final: 0.7404 (t0) REVERT: C 515 VAL cc_start: 0.8182 (OUTLIER) cc_final: 0.7855 (m) REVERT: C 542 MET cc_start: 0.8365 (ptt) cc_final: 0.8023 (ptt) REVERT: C 585 TRP cc_start: 0.8551 (p-90) cc_final: 0.8017 (p-90) REVERT: C 599 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.6116 (pmt-80) REVERT: C 634 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8424 (mm-40) REVERT: C 637 GLU cc_start: 0.7065 (tt0) cc_final: 0.6262 (tt0) REVERT: C 677 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7524 (mtpt) REVERT: C 682 LEU cc_start: 0.8516 (tp) cc_final: 0.8259 (tp) REVERT: C 687 GLN cc_start: 0.7984 (pt0) cc_final: 0.7614 (pm20) REVERT: C 693 GLN cc_start: 0.7224 (tp40) cc_final: 0.6579 (tp40) REVERT: C 792 ASP cc_start: 0.7870 (p0) cc_final: 0.7611 (p0) REVERT: C 808 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7522 (mm-30) REVERT: C 924 ASP cc_start: 0.8386 (m-30) cc_final: 0.8087 (t0) REVERT: C 945 ASN cc_start: 0.7739 (m-40) cc_final: 0.7395 (t0) REVERT: C 955 PHE cc_start: 0.8408 (p90) cc_final: 0.7882 (p90) REVERT: C 973 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7847 (ptm160) REVERT: C 997 ASP cc_start: 0.7203 (m-30) cc_final: 0.6849 (t0) REVERT: D 15 ASP cc_start: 0.8138 (m-30) cc_final: 0.7612 (t0) REVERT: D 62 TRP cc_start: 0.7978 (t60) cc_final: 0.7551 (t60) REVERT: D 67 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7387 (mp0) REVERT: D 75 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7409 (tm-30) REVERT: D 84 VAL cc_start: 0.8128 (t) cc_final: 0.7580 (p) REVERT: D 85 VAL cc_start: 0.8643 (t) cc_final: 0.8401 (p) REVERT: D 131 GLU cc_start: 0.6889 (tp30) cc_final: 0.6459 (tp30) REVERT: D 144 ASP cc_start: 0.8113 (m-30) cc_final: 0.7430 (m-30) REVERT: D 170 GLU cc_start: 0.6827 (pm20) cc_final: 0.6544 (pm20) REVERT: D 211 ASP cc_start: 0.7751 (t0) cc_final: 0.7302 (m-30) REVERT: D 243 GLU cc_start: 0.6924 (tt0) cc_final: 0.6620 (tt0) REVERT: D 245 GLN cc_start: 0.7221 (tt0) cc_final: 0.6937 (mt0) REVERT: D 288 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7163 (mtt180) REVERT: D 403 ASP cc_start: 0.7471 (m-30) cc_final: 0.6912 (m-30) REVERT: D 492 ASP cc_start: 0.7753 (t0) cc_final: 0.7303 (t0) REVERT: D 599 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.6267 (pmt-80) REVERT: D 634 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8525 (mm-40) REVERT: D 655 MET cc_start: 0.7830 (ttt) cc_final: 0.7580 (ttm) REVERT: D 677 LYS cc_start: 0.8404 (mtpt) cc_final: 0.7980 (mtpp) REVERT: D 693 GLN cc_start: 0.7159 (tp40) cc_final: 0.6813 (tp40) REVERT: D 699 ARG cc_start: 0.6696 (ptp-110) cc_final: 0.6452 (ptp-170) REVERT: D 709 SER cc_start: 0.8190 (t) cc_final: 0.7688 (p) REVERT: D 721 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7530 (ttm-80) REVERT: D 749 ILE cc_start: 0.7557 (tp) cc_final: 0.7095 (tp) REVERT: D 768 MET cc_start: 0.5738 (ttm) cc_final: 0.5443 (ttm) REVERT: D 924 ASP cc_start: 0.8262 (m-30) cc_final: 0.7893 (t0) REVERT: D 952 ARG cc_start: 0.7544 (ttm-80) cc_final: 0.7308 (ttm110) REVERT: D 955 PHE cc_start: 0.8401 (p90) cc_final: 0.7953 (p90) REVERT: D 973 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7885 (ptm160) REVERT: D 997 ASP cc_start: 0.7341 (m-30) cc_final: 0.6788 (t0) outliers start: 115 outliers final: 69 residues processed: 886 average time/residue: 0.4768 time to fit residues: 667.0081 Evaluate side-chains 878 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 797 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 181 GLU 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 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 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 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 362 LEU Chi-restraints excluded: chain B residue 417 THR 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 749 ILE Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 973 ARG 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 132 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 233 ASP 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 745 MET Chi-restraints excluded: chain C residue 782 ASP 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 973 ARG Chi-restraints excluded: chain C residue 977 HIS 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 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 362 LEU 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 637 GLU 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 777 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 973 ARG 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 401 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 289 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 395 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 138 optimal weight: 0.7980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** 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 ** 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 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 GLN ** 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** ** D 359 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.097580 restraints weight = 57676.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100954 restraints weight = 26956.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103142 restraints weight = 15443.536| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33792 Z= 0.156 Angle : 0.638 7.958 46104 Z= 0.329 Chirality : 0.046 0.315 4820 Planarity : 0.004 0.043 6088 Dihedral : 4.793 37.990 4477 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.35 % Allowed : 15.96 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.13), residues: 4080 helix: -1.86 (0.28), residues: 340 sheet: 0.11 (0.14), residues: 1432 loop : -2.33 (0.12), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 261 HIS 0.011 0.001 HIS C 844 PHE 0.013 0.001 PHE C 549 TYR 0.021 0.002 TYR C 161 ARG 0.009 0.001 ARG C 288 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 856) hydrogen bonds : angle 5.17568 ( 2448) covalent geometry : bond 0.00363 (33792) covalent geometry : angle 0.63802 (46104) *********************** 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 927 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 810 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.8966 (t) cc_final: 0.8617 (p) REVERT: A 46 ARG cc_start: 0.8254 (tpp80) cc_final: 0.8040 (ttm-80) REVERT: A 62 TRP cc_start: 0.8183 (t60) cc_final: 0.7620 (t60) REVERT: A 67 GLU cc_start: 0.7801 (mp0) cc_final: 0.7580 (mp0) REVERT: A 75 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7239 (tm-30) REVERT: A 84 VAL cc_start: 0.8171 (t) cc_final: 0.7606 (p) REVERT: A 85 VAL cc_start: 0.8741 (t) cc_final: 0.8477 (p) REVERT: A 131 GLU cc_start: 0.7473 (tp30) cc_final: 0.7078 (tp30) REVERT: A 144 ASP cc_start: 0.7979 (m-30) cc_final: 0.7351 (m-30) REVERT: A 187 MET cc_start: 0.8270 (ttp) cc_final: 0.8040 (ttp) REVERT: A 221 GLN cc_start: 0.8156 (pm20) cc_final: 0.7916 (pm20) REVERT: A 241 GLU cc_start: 0.7006 (pt0) cc_final: 0.6777 (mt-10) REVERT: A 243 GLU cc_start: 0.7033 (tt0) cc_final: 0.6783 (tt0) REVERT: A 288 ARG cc_start: 0.8044 (mtt-85) cc_final: 0.7396 (mtt-85) REVERT: A 338 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7220 (tm-30) REVERT: A 473 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7956 (tpt170) REVERT: A 492 ASP cc_start: 0.7904 (t0) cc_final: 0.7451 (t0) REVERT: A 585 TRP cc_start: 0.8807 (p-90) cc_final: 0.7765 (p-90) REVERT: A 599 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6689 (pmt-80) REVERT: A 634 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8474 (mm-40) REVERT: A 637 GLU cc_start: 0.7354 (tt0) cc_final: 0.6500 (tt0) REVERT: A 655 MET cc_start: 0.7895 (ttt) cc_final: 0.7610 (ttm) REVERT: A 677 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7539 (mtpt) REVERT: A 693 GLN cc_start: 0.7280 (tp40) cc_final: 0.6673 (tp-100) REVERT: A 721 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7268 (mtp-110) REVERT: A 739 HIS cc_start: 0.7507 (t-90) cc_final: 0.7088 (t-90) REVERT: A 748 CYS cc_start: 0.8304 (m) cc_final: 0.8025 (m) REVERT: A 749 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7270 (tp) REVERT: A 756 TRP cc_start: 0.7538 (m-90) cc_final: 0.6917 (m-90) REVERT: A 773 LYS cc_start: 0.6975 (tmmt) cc_final: 0.6758 (tmmt) REVERT: A 792 ASP cc_start: 0.7803 (p0) cc_final: 0.7518 (p0) REVERT: A 924 ASP cc_start: 0.8279 (m-30) cc_final: 0.8003 (p0) REVERT: A 935 ASN cc_start: 0.8870 (p0) cc_final: 0.8607 (p0) REVERT: A 945 ASN cc_start: 0.7519 (m-40) cc_final: 0.7219 (t0) REVERT: A 955 PHE cc_start: 0.8407 (p90) cc_final: 0.8204 (p90) REVERT: A 961 ARG cc_start: 0.7802 (tpt-90) cc_final: 0.7589 (ttt90) REVERT: A 973 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7645 (ptm160) REVERT: A 974 HIS cc_start: 0.7666 (p-80) cc_final: 0.7205 (p-80) REVERT: A 975 LEU cc_start: 0.8654 (mt) cc_final: 0.8166 (mt) REVERT: B 9 VAL cc_start: 0.9043 (m) cc_final: 0.8813 (p) REVERT: B 15 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7872 (t0) REVERT: B 62 TRP cc_start: 0.8080 (t60) cc_final: 0.7506 (t60) REVERT: B 67 GLU cc_start: 0.7814 (mp0) cc_final: 0.7537 (mp0) REVERT: B 84 VAL cc_start: 0.8265 (t) cc_final: 0.7693 (p) REVERT: B 85 VAL cc_start: 0.8683 (t) cc_final: 0.8422 (p) REVERT: B 92 MET cc_start: 0.8474 (mmm) cc_final: 0.7988 (mmm) REVERT: B 100 TYR cc_start: 0.7279 (t80) cc_final: 0.6354 (t80) REVERT: B 131 GLU cc_start: 0.7576 (tp30) cc_final: 0.7206 (tp30) REVERT: B 144 ASP cc_start: 0.8157 (m-30) cc_final: 0.7614 (m-30) REVERT: B 211 ASP cc_start: 0.7562 (t0) cc_final: 0.7220 (t0) REVERT: B 299 LYS cc_start: 0.8110 (mmmm) cc_final: 0.7689 (mttp) REVERT: B 338 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7429 (tm-30) REVERT: B 403 ASP cc_start: 0.7274 (m-30) cc_final: 0.6887 (m-30) REVERT: B 411 ASP cc_start: 0.7326 (t0) cc_final: 0.6923 (m-30) REVERT: B 412 GLU cc_start: 0.6914 (tt0) cc_final: 0.6573 (tt0) REVERT: B 492 ASP cc_start: 0.7913 (t0) cc_final: 0.7463 (t0) REVERT: B 544 ASN cc_start: 0.8422 (m-40) cc_final: 0.8193 (m-40) REVERT: B 578 TYR cc_start: 0.8693 (m-10) cc_final: 0.8485 (m-10) REVERT: B 585 TRP cc_start: 0.8568 (p-90) cc_final: 0.7754 (p-90) REVERT: B 599 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6336 (pmt-80) REVERT: B 634 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8607 (mm110) REVERT: B 637 GLU cc_start: 0.7219 (tt0) cc_final: 0.6693 (tt0) REVERT: B 655 MET cc_start: 0.7879 (ttt) cc_final: 0.7571 (ttm) REVERT: B 677 LYS cc_start: 0.8459 (mtpt) cc_final: 0.7837 (mtpt) REVERT: B 693 GLN cc_start: 0.7035 (tp40) cc_final: 0.6778 (tp40) REVERT: B 708 TRP cc_start: 0.8326 (p-90) cc_final: 0.7827 (p-90) REVERT: B 739 HIS cc_start: 0.7126 (t70) cc_final: 0.6429 (t-90) REVERT: B 908 ASP cc_start: 0.7806 (t0) cc_final: 0.7604 (t0) REVERT: B 919 ASP cc_start: 0.8073 (m-30) cc_final: 0.7627 (t0) REVERT: B 955 PHE cc_start: 0.8387 (p90) cc_final: 0.7829 (p90) REVERT: B 973 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7572 (ptm160) REVERT: B 997 ASP cc_start: 0.7394 (m-30) cc_final: 0.6961 (t0) REVERT: B 1016 TYR cc_start: 0.7194 (p90) cc_final: 0.6836 (p90) REVERT: C 9 VAL cc_start: 0.9054 (m) cc_final: 0.8845 (p) REVERT: C 15 ASP cc_start: 0.8267 (m-30) cc_final: 0.7849 (t0) REVERT: C 44 THR cc_start: 0.8893 (t) cc_final: 0.8471 (p) REVERT: C 46 ARG cc_start: 0.8264 (mtt180) cc_final: 0.7980 (ttm-80) REVERT: C 62 TRP cc_start: 0.8233 (t60) cc_final: 0.7759 (t60) REVERT: C 84 VAL cc_start: 0.8245 (t) cc_final: 0.7741 (p) REVERT: C 85 VAL cc_start: 0.8786 (t) cc_final: 0.8494 (p) REVERT: C 92 MET cc_start: 0.8237 (mmm) cc_final: 0.7729 (mmm) REVERT: C 136 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8083 (mp0) REVERT: C 144 ASP cc_start: 0.8009 (m-30) cc_final: 0.7187 (m-30) REVERT: C 187 MET cc_start: 0.8343 (ttp) cc_final: 0.8067 (ttp) REVERT: C 211 ASP cc_start: 0.7802 (t0) cc_final: 0.7446 (m-30) REVERT: C 221 GLN cc_start: 0.8287 (pm20) cc_final: 0.7721 (pm20) REVERT: C 237 ARG cc_start: 0.7483 (ttm-80) cc_final: 0.7072 (mtp85) REVERT: C 334 GLU cc_start: 0.6893 (tp30) cc_final: 0.6430 (tm-30) REVERT: C 349 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7505 (tp) REVERT: C 372 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6860 (mtm) REVERT: C 403 ASP cc_start: 0.7192 (m-30) cc_final: 0.6630 (m-30) REVERT: C 492 ASP cc_start: 0.7861 (t0) cc_final: 0.7496 (t0) REVERT: C 515 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.8035 (m) REVERT: C 599 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.6278 (pmt-80) REVERT: C 634 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8449 (mm-40) REVERT: C 637 GLU cc_start: 0.7089 (tt0) cc_final: 0.6277 (tt0) REVERT: C 677 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7570 (mtpt) REVERT: C 682 LEU cc_start: 0.8505 (tp) cc_final: 0.8271 (tp) REVERT: C 687 GLN cc_start: 0.8014 (pt0) cc_final: 0.7736 (pm20) REVERT: C 693 GLN cc_start: 0.7138 (tp40) cc_final: 0.6445 (tp40) REVERT: C 708 TRP cc_start: 0.8318 (p-90) cc_final: 0.6896 (p-90) REVERT: C 744 GLU cc_start: 0.8265 (pm20) cc_final: 0.7712 (pm20) REVERT: C 768 MET cc_start: 0.5477 (ptm) cc_final: 0.5249 (ptt) REVERT: C 790 ASP cc_start: 0.7417 (m-30) cc_final: 0.7151 (t0) REVERT: C 792 ASP cc_start: 0.7850 (p0) cc_final: 0.7605 (p0) REVERT: C 808 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7536 (mm-30) REVERT: C 924 ASP cc_start: 0.8388 (m-30) cc_final: 0.8101 (t0) REVERT: C 945 ASN cc_start: 0.7804 (m-40) cc_final: 0.7462 (t0) REVERT: C 955 PHE cc_start: 0.8473 (p90) cc_final: 0.7914 (p90) REVERT: C 973 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7832 (ptm160) REVERT: C 997 ASP cc_start: 0.7106 (m-30) cc_final: 0.6720 (t0) REVERT: D 15 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7825 (t0) REVERT: D 62 TRP cc_start: 0.8147 (t60) cc_final: 0.7694 (t60) REVERT: D 67 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7456 (mp0) REVERT: D 75 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7419 (tm-30) REVERT: D 84 VAL cc_start: 0.8197 (t) cc_final: 0.7682 (p) REVERT: D 85 VAL cc_start: 0.8697 (t) cc_final: 0.8485 (p) REVERT: D 100 TYR cc_start: 0.7172 (t80) cc_final: 0.6267 (t80) REVERT: D 131 GLU cc_start: 0.7004 (tp30) cc_final: 0.6550 (tp30) REVERT: D 144 ASP cc_start: 0.8130 (m-30) cc_final: 0.7515 (m-30) REVERT: D 170 GLU cc_start: 0.6804 (pm20) cc_final: 0.6576 (pm20) REVERT: D 211 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: D 243 GLU cc_start: 0.6961 (tt0) cc_final: 0.6647 (tt0) REVERT: D 245 GLN cc_start: 0.7214 (tt0) cc_final: 0.6942 (mt0) REVERT: D 288 ARG cc_start: 0.7629 (mtt180) cc_final: 0.7159 (mtt180) REVERT: D 403 ASP cc_start: 0.7460 (m-30) cc_final: 0.6979 (m-30) REVERT: D 492 ASP cc_start: 0.7838 (t0) cc_final: 0.7438 (t0) REVERT: D 599 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6501 (pmt-80) REVERT: D 634 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8542 (mm-40) REVERT: D 655 MET cc_start: 0.7883 (ttt) cc_final: 0.7615 (ttm) REVERT: D 677 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8044 (mtpp) REVERT: D 693 GLN cc_start: 0.7175 (tp40) cc_final: 0.6844 (tp40) REVERT: D 699 ARG cc_start: 0.6800 (ptp-110) cc_final: 0.6586 (ptp-170) REVERT: D 709 SER cc_start: 0.8141 (t) cc_final: 0.7526 (p) REVERT: D 721 ARG cc_start: 0.7774 (ttm110) cc_final: 0.7543 (ttm-80) REVERT: D 739 HIS cc_start: 0.7352 (t-90) cc_final: 0.7109 (t70) REVERT: D 744 GLU cc_start: 0.8279 (pm20) cc_final: 0.7701 (pm20) REVERT: D 768 MET cc_start: 0.5847 (ttm) cc_final: 0.5293 (ttm) REVERT: D 924 ASP cc_start: 0.8267 (m-30) cc_final: 0.7919 (t0) REVERT: D 952 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7380 (ttm110) REVERT: D 973 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7851 (ptm160) REVERT: D 997 ASP cc_start: 0.7373 (m-30) cc_final: 0.6750 (t0) REVERT: D 1019 VAL cc_start: 0.8591 (t) cc_final: 0.8101 (p) outliers start: 117 outliers final: 83 residues processed: 872 average time/residue: 0.4615 time to fit residues: 627.9787 Evaluate side-chains 899 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 801 time to evaluate : 3.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 181 GLU 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 737 ILE Chi-restraints excluded: chain A residue 749 ILE 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 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 1017 GLN 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 241 GLU Chi-restraints excluded: chain B residue 266 GLN 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 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 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 801 ILE Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 973 ARG Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 233 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 372 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 745 MET 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 973 ARG Chi-restraints excluded: chain C residue 977 HIS 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 230 ARG Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 362 LEU 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 637 GLU 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 777 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 829 THR 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 973 ARG Chi-restraints excluded: chain D residue 977 HIS Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1017 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 369 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 330 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 346 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 398 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 604 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 HIS ** 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 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 903 GLN ** 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.096733 restraints weight = 57595.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.100093 restraints weight = 26969.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102256 restraints weight = 15452.111| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33792 Z= 0.178 Angle : 0.665 9.913 46104 Z= 0.344 Chirality : 0.047 0.270 4820 Planarity : 0.004 0.042 6088 Dihedral : 4.932 38.843 4477 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.00 % Allowed : 16.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.13), residues: 4080 helix: -1.78 (0.28), residues: 340 sheet: 0.07 (0.14), residues: 1420 loop : -2.35 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 90 HIS 0.014 0.001 HIS B 974 PHE 0.016 0.002 PHE C 549 TYR 0.022 0.002 TYR C 161 ARG 0.009 0.001 ARG D 46 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 856) hydrogen bonds : angle 5.20996 ( 2448) covalent geometry : bond 0.00412 (33792) covalent geometry : angle 0.66516 (46104) *********************** 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 954 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 814 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8531 (mtm110) cc_final: 0.8064 (ttm-80) REVERT: A 44 THR cc_start: 0.8918 (t) cc_final: 0.8606 (p) REVERT: A 62 TRP cc_start: 0.8281 (t60) cc_final: 0.7765 (t60) REVERT: A 67 GLU cc_start: 0.7807 (mp0) cc_final: 0.7596 (mp0) REVERT: A 75 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7193 (tm-30) REVERT: A 84 VAL cc_start: 0.8180 (t) cc_final: 0.7662 (p) REVERT: A 85 VAL cc_start: 0.8755 (t) cc_final: 0.8497 (p) REVERT: A 136 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7850 (mp0) REVERT: A 144 ASP cc_start: 0.7981 (m-30) cc_final: 0.7351 (m-30) REVERT: A 161 TYR cc_start: 0.7912 (t80) cc_final: 0.7674 (t80) REVERT: A 241 GLU cc_start: 0.6995 (pt0) cc_final: 0.6768 (mt-10) REVERT: A 243 GLU cc_start: 0.7036 (tt0) cc_final: 0.6784 (tt0) REVERT: A 473 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7972 (tpt170) REVERT: A 492 ASP cc_start: 0.7963 (t0) cc_final: 0.7588 (t0) REVERT: A 599 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6800 (pmt-80) REVERT: A 634 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8501 (mm-40) REVERT: A 637 GLU cc_start: 0.7359 (tt0) cc_final: 0.6709 (tt0) REVERT: A 655 MET cc_start: 0.7888 (ttt) cc_final: 0.7609 (ttm) REVERT: A 677 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7523 (mtpt) REVERT: A 687 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: A 693 GLN cc_start: 0.7319 (tp40) cc_final: 0.6847 (tp-100) REVERT: A 708 TRP cc_start: 0.8418 (p-90) cc_final: 0.8018 (p-90) REVERT: A 721 ARG cc_start: 0.7782 (ttm-80) cc_final: 0.7342 (mtp-110) REVERT: A 739 HIS cc_start: 0.7608 (t-90) cc_final: 0.7195 (t-90) REVERT: A 749 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7367 (tp) REVERT: A 756 TRP cc_start: 0.7565 (m-90) cc_final: 0.6833 (m-90) REVERT: A 773 LYS cc_start: 0.7050 (tmmt) cc_final: 0.6797 (tmmt) REVERT: A 792 ASP cc_start: 0.7764 (p0) cc_final: 0.7495 (p0) REVERT: A 924 ASP cc_start: 0.8277 (m-30) cc_final: 0.7998 (p0) REVERT: A 935 ASN cc_start: 0.8906 (p0) cc_final: 0.8614 (p0) REVERT: A 945 ASN cc_start: 0.7581 (m-40) cc_final: 0.7249 (t0) REVERT: A 961 ARG cc_start: 0.7831 (tpt-90) cc_final: 0.7612 (ttt90) REVERT: A 973 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7700 (ptm160) REVERT: A 974 HIS cc_start: 0.7666 (p-80) cc_final: 0.7205 (p-80) REVERT: A 975 LEU cc_start: 0.8651 (mt) cc_final: 0.8170 (mt) REVERT: A 1019 VAL cc_start: 0.8557 (t) cc_final: 0.8134 (p) REVERT: B 9 VAL cc_start: 0.9117 (m) cc_final: 0.8882 (p) REVERT: B 15 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7902 (t0) REVERT: B 62 TRP cc_start: 0.8114 (t60) cc_final: 0.7574 (t60) REVERT: B 67 GLU cc_start: 0.7855 (mp0) cc_final: 0.7560 (mp0) REVERT: B 84 VAL cc_start: 0.8255 (t) cc_final: 0.7668 (p) REVERT: B 85 VAL cc_start: 0.8700 (t) cc_final: 0.8442 (p) REVERT: B 92 MET cc_start: 0.8448 (mmm) cc_final: 0.8181 (mmt) REVERT: B 100 TYR cc_start: 0.7342 (t80) cc_final: 0.6332 (t80) REVERT: B 131 GLU cc_start: 0.7781 (tp30) cc_final: 0.7483 (tp30) REVERT: B 136 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7850 (mp0) REVERT: B 144 ASP cc_start: 0.8151 (m-30) cc_final: 0.7594 (m-30) REVERT: B 211 ASP cc_start: 0.7560 (t0) cc_final: 0.7215 (t0) REVERT: B 237 ARG cc_start: 0.7382 (mtp85) cc_final: 0.6437 (mtp85) REVERT: B 299 LYS cc_start: 0.8116 (mmmm) cc_final: 0.7696 (mttp) REVERT: B 403 ASP cc_start: 0.7323 (m-30) cc_final: 0.6900 (m-30) REVERT: B 412 GLU cc_start: 0.6924 (tt0) cc_final: 0.6688 (tt0) REVERT: B 492 ASP cc_start: 0.7961 (t0) cc_final: 0.7534 (t0) REVERT: B 544 ASN cc_start: 0.8463 (m-40) cc_final: 0.8172 (m-40) REVERT: B 585 TRP cc_start: 0.8596 (p-90) cc_final: 0.7639 (p-90) REVERT: B 599 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6357 (pmt-80) REVERT: B 634 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8630 (mm110) REVERT: B 637 GLU cc_start: 0.7255 (tt0) cc_final: 0.6831 (tt0) REVERT: B 655 MET cc_start: 0.7876 (ttt) cc_final: 0.7556 (ttm) REVERT: B 672 VAL cc_start: 0.8480 (m) cc_final: 0.8257 (t) REVERT: B 677 LYS cc_start: 0.8486 (mtpt) cc_final: 0.7896 (mtpt) REVERT: B 693 GLN cc_start: 0.7014 (tp40) cc_final: 0.6542 (tp-100) REVERT: B 708 TRP cc_start: 0.8289 (p-90) cc_final: 0.7770 (p-90) REVERT: B 721 ARG cc_start: 0.7272 (mtp180) cc_final: 0.6777 (ttm-80) REVERT: B 739 HIS cc_start: 0.7294 (t70) cc_final: 0.6997 (t70) REVERT: B 905 ASN cc_start: 0.7057 (p0) cc_final: 0.6825 (p0) REVERT: B 919 ASP cc_start: 0.8094 (m-30) cc_final: 0.7393 (t0) REVERT: B 955 PHE cc_start: 0.8413 (p90) cc_final: 0.7873 (p90) REVERT: B 973 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7697 (ptm160) REVERT: B 983 TRP cc_start: 0.8012 (m100) cc_final: 0.7646 (m-10) REVERT: B 997 ASP cc_start: 0.7361 (m-30) cc_final: 0.6909 (t0) REVERT: B 1016 TYR cc_start: 0.7271 (p90) cc_final: 0.6836 (p90) REVERT: C 9 VAL cc_start: 0.9142 (m) cc_final: 0.8929 (p) REVERT: C 15 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7886 (t0) REVERT: C 43 ARG cc_start: 0.8540 (mtm110) cc_final: 0.8171 (mtm-85) REVERT: C 44 THR cc_start: 0.8877 (t) cc_final: 0.8500 (p) REVERT: C 46 ARG cc_start: 0.8266 (mtt180) cc_final: 0.7941 (ttm-80) REVERT: C 62 TRP cc_start: 0.8274 (t60) cc_final: 0.7796 (t60) REVERT: C 84 VAL cc_start: 0.8271 (t) cc_final: 0.7753 (p) REVERT: C 85 VAL cc_start: 0.8746 (t) cc_final: 0.8457 (p) REVERT: C 92 MET cc_start: 0.8264 (mmm) cc_final: 0.7747 (mmm) REVERT: C 144 ASP cc_start: 0.8003 (m-30) cc_final: 0.7218 (m-30) REVERT: C 211 ASP cc_start: 0.7801 (t0) cc_final: 0.7294 (m-30) REVERT: C 221 GLN cc_start: 0.8314 (pm20) cc_final: 0.7752 (pm20) REVERT: C 237 ARG cc_start: 0.7469 (ttm-80) cc_final: 0.7017 (mtp85) REVERT: C 245 GLN cc_start: 0.6688 (tp40) cc_final: 0.6469 (tp40) REVERT: C 334 GLU cc_start: 0.6993 (tp30) cc_final: 0.6504 (tm-30) REVERT: C 349 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7538 (tp) REVERT: C 403 ASP cc_start: 0.7190 (m-30) cc_final: 0.6635 (m-30) REVERT: C 461 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7252 (mm-30) REVERT: C 492 ASP cc_start: 0.7901 (t0) cc_final: 0.7590 (t0) REVERT: C 515 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8078 (m) REVERT: C 599 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6319 (pmt-80) REVERT: C 634 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8528 (mm-40) REVERT: C 637 GLU cc_start: 0.7101 (tt0) cc_final: 0.6233 (tt0) REVERT: C 677 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7538 (mtpt) REVERT: C 687 GLN cc_start: 0.8046 (pt0) cc_final: 0.7639 (pm20) REVERT: C 693 GLN cc_start: 0.7300 (tp40) cc_final: 0.6741 (tp40) REVERT: C 708 TRP cc_start: 0.8318 (p-90) cc_final: 0.6959 (p-90) REVERT: C 744 GLU cc_start: 0.8251 (pm20) cc_final: 0.7813 (pm20) REVERT: C 761 GLN cc_start: 0.7023 (mm110) cc_final: 0.6590 (mp10) REVERT: C 792 ASP cc_start: 0.7808 (p0) cc_final: 0.7543 (p0) REVERT: C 808 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7568 (mm-30) REVERT: C 924 ASP cc_start: 0.8424 (m-30) cc_final: 0.8098 (t0) REVERT: C 955 PHE cc_start: 0.8543 (p90) cc_final: 0.7933 (p90) REVERT: C 973 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7709 (ptt180) REVERT: C 997 ASP cc_start: 0.7091 (m-30) cc_final: 0.6694 (t0) REVERT: C 1019 VAL cc_start: 0.8463 (t) cc_final: 0.8022 (p) REVERT: D 15 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7854 (t0) REVERT: D 62 TRP cc_start: 0.8216 (t60) cc_final: 0.7793 (t60) REVERT: D 67 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7494 (mp0) REVERT: D 75 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7379 (tm-30) REVERT: D 84 VAL cc_start: 0.8236 (t) cc_final: 0.7723 (p) REVERT: D 85 VAL cc_start: 0.8700 (t) cc_final: 0.8494 (p) REVERT: D 90 TRP cc_start: 0.7855 (p90) cc_final: 0.7651 (p90) REVERT: D 100 TYR cc_start: 0.7219 (t80) cc_final: 0.6237 (t80) REVERT: D 131 GLU cc_start: 0.7104 (tp30) cc_final: 0.6650 (tp30) REVERT: D 144 ASP cc_start: 0.8124 (m-30) cc_final: 0.7493 (m-30) REVERT: D 170 GLU cc_start: 0.6887 (pm20) cc_final: 0.6614 (pm20) REVERT: D 211 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: D 243 GLU cc_start: 0.6972 (tt0) cc_final: 0.6658 (tt0) REVERT: D 245 GLN cc_start: 0.7219 (tt0) cc_final: 0.6925 (mt0) REVERT: D 288 ARG cc_start: 0.7596 (mtt180) cc_final: 0.7162 (mtt180) REVERT: D 403 ASP cc_start: 0.7480 (m-30) cc_final: 0.6995 (m-30) REVERT: D 492 ASP cc_start: 0.7877 (t0) cc_final: 0.7537 (t0) REVERT: D 599 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6579 (pmt-80) REVERT: D 634 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8551 (mm-40) REVERT: D 655 MET cc_start: 0.7860 (ttt) cc_final: 0.7614 (ttm) REVERT: D 677 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8045 (mtpp) REVERT: D 693 GLN cc_start: 0.7158 (tp-100) cc_final: 0.6866 (tp40) REVERT: D 744 GLU cc_start: 0.8324 (pm20) cc_final: 0.7862 (pm20) REVERT: D 768 MET cc_start: 0.5752 (ttm) cc_final: 0.5214 (ttm) REVERT: D 898 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6420 (tp) REVERT: D 917 ARG cc_start: 0.7078 (mmt90) cc_final: 0.6725 (mtt-85) REVERT: D 924 ASP cc_start: 0.8288 (m-30) cc_final: 0.8026 (t0) REVERT: D 952 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7375 (ttm110) REVERT: D 973 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7707 (ptm160) REVERT: D 997 ASP cc_start: 0.7335 (m-30) cc_final: 0.6655 (t0) REVERT: D 1019 VAL cc_start: 0.8613 (t) cc_final: 0.8193 (p) outliers start: 140 outliers final: 102 residues processed: 888 average time/residue: 0.4811 time to fit residues: 667.4338 Evaluate side-chains 905 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 786 time to evaluate : 3.747 ------------------------------------------------------------------------------- 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 132 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 308 LEU 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 687 GLN 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 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 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 266 GLN 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 370 GLN 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 737 ILE Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 838 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 959 ILE Chi-restraints excluded: chain B residue 973 ARG Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1017 GLN Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain C residue 417 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 737 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 973 ARG Chi-restraints excluded: chain C residue 977 HIS 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 230 ARG Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 362 LEU 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 663 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 898 LEU Chi-restraints excluded: chain D residue 925 MET Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 973 ARG Chi-restraints excluded: chain D residue 977 HIS Chi-restraints excluded: chain D residue 984 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 31 optimal weight: 5.9990 chunk 342 optimal weight: 3.9990 chunk 401 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 374 optimal weight: 0.0070 chunk 373 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 339 optimal weight: 3.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** 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 ** 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 890 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.098951 restraints weight = 57131.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102290 restraints weight = 26953.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.104479 restraints weight = 15535.227| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33792 Z= 0.122 Angle : 0.640 9.438 46104 Z= 0.326 Chirality : 0.045 0.216 4820 Planarity : 0.004 0.040 6088 Dihedral : 4.731 39.807 4477 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.18 % Allowed : 17.99 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.13), residues: 4080 helix: -1.61 (0.28), residues: 340 sheet: 0.14 (0.14), residues: 1432 loop : -2.24 (0.12), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 842 HIS 0.014 0.001 HIS B 974 PHE 0.010 0.001 PHE C 549 TYR 0.021 0.001 TYR C 161 ARG 0.009 0.000 ARG A 800 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 856) hydrogen bonds : angle 4.98180 ( 2448) covalent geometry : bond 0.00281 (33792) covalent geometry : angle 0.63993 (46104) *********************** 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 914 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 803 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8486 (mtm110) cc_final: 0.8072 (ttm-80) REVERT: A 44 THR cc_start: 0.8969 (t) cc_final: 0.8598 (p) REVERT: A 62 TRP cc_start: 0.8188 (t60) cc_final: 0.7720 (t60) REVERT: A 67 GLU cc_start: 0.7756 (mp0) cc_final: 0.7538 (mp0) REVERT: A 75 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7207 (tm-30) REVERT: A 84 VAL cc_start: 0.8158 (t) cc_final: 0.7599 (p) REVERT: A 85 VAL cc_start: 0.8732 (t) cc_final: 0.8481 (p) REVERT: A 136 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7950 (mp0) REVERT: A 144 ASP cc_start: 0.7947 (m-30) cc_final: 0.7218 (m-30) REVERT: A 161 TYR cc_start: 0.7888 (t80) cc_final: 0.7623 (t80) REVERT: A 241 GLU cc_start: 0.6944 (pt0) cc_final: 0.6698 (mt-10) REVERT: A 243 GLU cc_start: 0.7004 (tt0) cc_final: 0.6750 (tt0) REVERT: A 245 GLN cc_start: 0.6608 (tp40) cc_final: 0.6272 (tp40) REVERT: A 492 ASP cc_start: 0.7888 (t0) cc_final: 0.7464 (t0) REVERT: A 585 TRP cc_start: 0.8833 (p-90) cc_final: 0.7722 (p-90) REVERT: A 599 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6686 (pmt-80) REVERT: A 634 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8493 (mm-40) REVERT: A 637 GLU cc_start: 0.7320 (tt0) cc_final: 0.6621 (tt0) REVERT: A 655 MET cc_start: 0.7872 (ttt) cc_final: 0.7600 (ttm) REVERT: A 677 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7512 (mtpt) REVERT: A 687 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: A 693 GLN cc_start: 0.7314 (tp40) cc_final: 0.6839 (tp-100) REVERT: A 708 TRP cc_start: 0.8420 (p-90) cc_final: 0.8009 (p-90) REVERT: A 721 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7279 (mtp-110) REVERT: A 739 HIS cc_start: 0.7541 (t-90) cc_final: 0.7232 (t-90) REVERT: A 749 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7341 (tp) REVERT: A 756 TRP cc_start: 0.7506 (m-90) cc_final: 0.6899 (m-90) REVERT: A 773 LYS cc_start: 0.7040 (tmmt) cc_final: 0.6801 (tmmt) REVERT: A 792 ASP cc_start: 0.7737 (p0) cc_final: 0.7476 (p0) REVERT: A 924 ASP cc_start: 0.8240 (m-30) cc_final: 0.8000 (p0) REVERT: A 935 ASN cc_start: 0.8873 (p0) cc_final: 0.8592 (p0) REVERT: A 945 ASN cc_start: 0.7469 (m-40) cc_final: 0.7163 (t0) REVERT: A 961 ARG cc_start: 0.7812 (tpt-90) cc_final: 0.7598 (ttt90) REVERT: A 973 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7521 (ptm160) REVERT: A 974 HIS cc_start: 0.7633 (p-80) cc_final: 0.7155 (p-80) REVERT: A 975 LEU cc_start: 0.8621 (mt) cc_final: 0.8145 (mt) REVERT: B 9 VAL cc_start: 0.9114 (m) cc_final: 0.8893 (p) REVERT: B 15 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7658 (t0) REVERT: B 62 TRP cc_start: 0.8043 (t60) cc_final: 0.7466 (t60) REVERT: B 67 GLU cc_start: 0.7789 (mp0) cc_final: 0.7489 (mp0) REVERT: B 84 VAL cc_start: 0.8225 (t) cc_final: 0.7645 (p) REVERT: B 85 VAL cc_start: 0.8684 (t) cc_final: 0.8431 (p) REVERT: B 92 MET cc_start: 0.8460 (mmm) cc_final: 0.8207 (mmm) REVERT: B 131 GLU cc_start: 0.7767 (tp30) cc_final: 0.7483 (tp30) REVERT: B 144 ASP cc_start: 0.8130 (m-30) cc_final: 0.7397 (m-30) REVERT: B 211 ASP cc_start: 0.7549 (t0) cc_final: 0.7199 (m-30) REVERT: B 237 ARG cc_start: 0.7336 (mtp85) cc_final: 0.6348 (mtp85) REVERT: B 403 ASP cc_start: 0.7309 (m-30) cc_final: 0.6903 (m-30) REVERT: B 411 ASP cc_start: 0.7199 (t0) cc_final: 0.6885 (m-30) REVERT: B 412 GLU cc_start: 0.6835 (tt0) cc_final: 0.6440 (tt0) REVERT: B 492 ASP cc_start: 0.7914 (t0) cc_final: 0.7465 (t0) REVERT: B 544 ASN cc_start: 0.8419 (m-40) cc_final: 0.8145 (m-40) REVERT: B 585 TRP cc_start: 0.8669 (p-90) cc_final: 0.7831 (p-90) REVERT: B 599 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.6235 (pmt-80) REVERT: B 634 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8606 (mm110) REVERT: B 637 GLU cc_start: 0.7215 (tt0) cc_final: 0.6623 (tt0) REVERT: B 655 MET cc_start: 0.7841 (ttt) cc_final: 0.7532 (ttm) REVERT: B 667 GLU cc_start: 0.7170 (pm20) cc_final: 0.6898 (pm20) REVERT: B 677 LYS cc_start: 0.8438 (mtpt) cc_final: 0.7697 (mtpt) REVERT: B 693 GLN cc_start: 0.6937 (tp40) cc_final: 0.6567 (tp-100) REVERT: B 721 ARG cc_start: 0.7183 (mtp180) cc_final: 0.6698 (ttm-80) REVERT: B 739 HIS cc_start: 0.7467 (t70) cc_final: 0.7091 (t-90) REVERT: B 905 ASN cc_start: 0.6948 (p0) cc_final: 0.6718 (p0) REVERT: B 973 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7424 (ptm160) REVERT: B 983 TRP cc_start: 0.7952 (m100) cc_final: 0.7726 (m100) REVERT: B 997 ASP cc_start: 0.7377 (m-30) cc_final: 0.6913 (t0) REVERT: B 1016 TYR cc_start: 0.7123 (p90) cc_final: 0.6796 (p90) REVERT: C 15 ASP cc_start: 0.8285 (m-30) cc_final: 0.7891 (t0) REVERT: C 43 ARG cc_start: 0.8532 (mtm110) cc_final: 0.8227 (mtm-85) REVERT: C 44 THR cc_start: 0.8882 (t) cc_final: 0.8657 (p) REVERT: C 62 TRP cc_start: 0.8171 (t60) cc_final: 0.7742 (t60) REVERT: C 84 VAL cc_start: 0.8232 (t) cc_final: 0.7740 (p) REVERT: C 85 VAL cc_start: 0.8781 (t) cc_final: 0.8495 (p) REVERT: C 92 MET cc_start: 0.8242 (mmm) cc_final: 0.7731 (mmm) REVERT: C 144 ASP cc_start: 0.7963 (m-30) cc_final: 0.7189 (m-30) REVERT: C 211 ASP cc_start: 0.7752 (t0) cc_final: 0.7257 (m-30) REVERT: C 237 ARG cc_start: 0.7407 (ttm-80) cc_final: 0.7095 (mtp85) REVERT: C 245 GLN cc_start: 0.6662 (tp40) cc_final: 0.6461 (tp40) REVERT: C 334 GLU cc_start: 0.6873 (tp30) cc_final: 0.6464 (tm-30) REVERT: C 349 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7489 (tp) REVERT: C 403 ASP cc_start: 0.7147 (m-30) cc_final: 0.6588 (m-30) REVERT: C 461 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7229 (mm-30) REVERT: C 492 ASP cc_start: 0.7805 (t0) cc_final: 0.7442 (t0) REVERT: C 515 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8030 (m) REVERT: C 542 MET cc_start: 0.8293 (ptt) cc_final: 0.8050 (ptt) REVERT: C 599 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.6218 (pmt-80) REVERT: C 634 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8507 (mm-40) REVERT: C 637 GLU cc_start: 0.7077 (tt0) cc_final: 0.6363 (tt0) REVERT: C 677 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7513 (mtpp) REVERT: C 693 GLN cc_start: 0.7231 (tp40) cc_final: 0.6723 (tp40) REVERT: C 708 TRP cc_start: 0.8316 (p-90) cc_final: 0.6948 (p-90) REVERT: C 744 GLU cc_start: 0.8224 (pm20) cc_final: 0.7814 (pm20) REVERT: C 757 GLN cc_start: 0.7667 (mt0) cc_final: 0.7087 (mt0) REVERT: C 761 GLN cc_start: 0.7012 (mm110) cc_final: 0.6679 (mp10) REVERT: C 792 ASP cc_start: 0.7790 (p0) cc_final: 0.7521 (p0) REVERT: C 808 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7533 (mm-30) REVERT: C 924 ASP cc_start: 0.8388 (m-30) cc_final: 0.8083 (t0) REVERT: C 945 ASN cc_start: 0.7744 (m-40) cc_final: 0.7442 (t0) REVERT: C 955 PHE cc_start: 0.8447 (p90) cc_final: 0.7900 (p90) REVERT: C 973 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7613 (ptm160) REVERT: C 997 ASP cc_start: 0.7093 (m-30) cc_final: 0.6738 (t0) REVERT: D 15 ASP cc_start: 0.8305 (m-30) cc_final: 0.7840 (t0) REVERT: D 62 TRP cc_start: 0.8102 (t60) cc_final: 0.7734 (t60) REVERT: D 67 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7428 (mp0) REVERT: D 75 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7369 (tm-30) REVERT: D 84 VAL cc_start: 0.8226 (t) cc_final: 0.7719 (p) REVERT: D 85 VAL cc_start: 0.8658 (t) cc_final: 0.8436 (p) REVERT: D 144 ASP cc_start: 0.8094 (m-30) cc_final: 0.7458 (m-30) REVERT: D 170 GLU cc_start: 0.6915 (pm20) cc_final: 0.6686 (pm20) REVERT: D 211 ASP cc_start: 0.7712 (t0) cc_final: 0.7328 (m-30) REVERT: D 243 GLU cc_start: 0.6930 (tt0) cc_final: 0.6634 (tt0) REVERT: D 245 GLN cc_start: 0.7199 (tt0) cc_final: 0.6894 (mt0) REVERT: D 288 ARG cc_start: 0.7634 (mtt180) cc_final: 0.7218 (mtt180) REVERT: D 403 ASP cc_start: 0.7393 (m-30) cc_final: 0.7005 (m-30) REVERT: D 492 ASP cc_start: 0.7809 (t0) cc_final: 0.7450 (t0) REVERT: D 599 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6566 (pmt-80) REVERT: D 634 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8528 (mm-40) REVERT: D 655 MET cc_start: 0.7819 (ttt) cc_final: 0.7580 (ttm) REVERT: D 677 LYS cc_start: 0.8404 (mtpt) cc_final: 0.8006 (mtpp) REVERT: D 744 GLU cc_start: 0.8331 (pm20) cc_final: 0.7913 (pm20) REVERT: D 768 MET cc_start: 0.5622 (ttm) cc_final: 0.5117 (ttm) REVERT: D 874 SER cc_start: 0.9285 (m) cc_final: 0.8867 (p) REVERT: D 898 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6345 (tp) REVERT: D 917 ARG cc_start: 0.7065 (mmt90) cc_final: 0.6710 (mtt-85) REVERT: D 924 ASP cc_start: 0.8248 (m-30) cc_final: 0.7888 (t0) REVERT: D 952 ARG cc_start: 0.7603 (ttm-80) cc_final: 0.7373 (ttm110) REVERT: D 973 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7561 (ptm160) REVERT: D 997 ASP cc_start: 0.7327 (m-30) cc_final: 0.6726 (t0) outliers start: 111 outliers final: 83 residues processed: 861 average time/residue: 0.4757 time to fit residues: 639.0856 Evaluate side-chains 893 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 796 time to evaluate : 3.912 ------------------------------------------------------------------------------- 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 181 GLU 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 687 GLN 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 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 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 323 ILE Chi-restraints excluded: chain B residue 362 LEU 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 745 MET Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 838 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 959 ILE Chi-restraints excluded: chain B residue 973 ARG 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 120 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 323 ILE 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 745 MET Chi-restraints excluded: chain C residue 782 ASP 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 973 ARG 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 663 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 898 LEU Chi-restraints excluded: chain D residue 925 MET Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 973 ARG Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1017 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 56 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 406 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 405 optimal weight: 0.0670 chunk 28 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 291 optimal weight: 0.9980 chunk 217 optimal weight: 6.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- 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 540 HIS A 604 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 HIS ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 HIS ** B 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 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 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 974 HIS ** 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 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 840 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.116407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.098661 restraints weight = 57097.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102063 restraints weight = 26682.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.104265 restraints weight = 15211.596| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33792 Z= 0.124 Angle : 0.642 9.483 46104 Z= 0.327 Chirality : 0.045 0.255 4820 Planarity : 0.004 0.053 6088 Dihedral : 4.640 39.383 4477 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.03 % Allowed : 18.54 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.13), residues: 4080 helix: -1.49 (0.29), residues: 340 sheet: 0.20 (0.14), residues: 1428 loop : -2.20 (0.12), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 842 HIS 0.014 0.001 HIS B 974 PHE 0.011 0.001 PHE C 549 TYR 0.021 0.001 TYR C 161 ARG 0.009 0.000 ARG A 800 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 856) hydrogen bonds : angle 4.88921 ( 2448) covalent geometry : bond 0.00289 (33792) covalent geometry : angle 0.64191 (46104) *********************** 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 902 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 796 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8498 (mtm110) cc_final: 0.8079 (ttm-80) REVERT: A 62 TRP cc_start: 0.8192 (t60) cc_final: 0.7709 (t60) REVERT: A 67 GLU cc_start: 0.7808 (mp0) cc_final: 0.7585 (mp0) REVERT: A 75 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7231 (tm-30) REVERT: A 84 VAL cc_start: 0.8114 (t) cc_final: 0.7549 (p) REVERT: A 85 VAL cc_start: 0.8719 (t) cc_final: 0.8463 (p) REVERT: A 144 ASP cc_start: 0.7951 (m-30) cc_final: 0.7195 (m-30) REVERT: A 161 TYR cc_start: 0.7890 (t80) cc_final: 0.7494 (t80) REVERT: A 241 GLU cc_start: 0.7045 (pt0) cc_final: 0.6614 (mt-10) REVERT: A 243 GLU cc_start: 0.7025 (tt0) cc_final: 0.6759 (tt0) REVERT: A 245 GLN cc_start: 0.6629 (tp40) cc_final: 0.6275 (tp40) REVERT: A 338 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7214 (tm-30) REVERT: A 492 ASP cc_start: 0.7882 (t0) cc_final: 0.7449 (t0) REVERT: A 585 TRP cc_start: 0.8811 (p-90) cc_final: 0.7692 (p-90) REVERT: A 599 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6689 (pmt-80) REVERT: A 634 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8501 (mm110) REVERT: A 637 GLU cc_start: 0.7347 (tt0) cc_final: 0.6611 (tt0) REVERT: A 655 MET cc_start: 0.7874 (ttt) cc_final: 0.7598 (ttm) REVERT: A 677 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7525 (mtpt) REVERT: A 687 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: A 693 GLN cc_start: 0.7327 (tp40) cc_final: 0.6848 (tp-100) REVERT: A 708 TRP cc_start: 0.8445 (p-90) cc_final: 0.8023 (p-90) REVERT: A 721 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.7269 (mtp-110) REVERT: A 739 HIS cc_start: 0.7572 (t-90) cc_final: 0.7287 (t-90) REVERT: A 749 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7306 (tp) REVERT: A 756 TRP cc_start: 0.7466 (m-90) cc_final: 0.6880 (m-90) REVERT: A 792 ASP cc_start: 0.7730 (p0) cc_final: 0.7480 (p0) REVERT: A 924 ASP cc_start: 0.8256 (m-30) cc_final: 0.8002 (p0) REVERT: A 935 ASN cc_start: 0.8864 (p0) cc_final: 0.8579 (p0) REVERT: A 945 ASN cc_start: 0.7455 (m-40) cc_final: 0.7162 (t0) REVERT: A 961 ARG cc_start: 0.7817 (tpt-90) cc_final: 0.7612 (ttt90) REVERT: A 973 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7533 (ptm160) REVERT: A 974 HIS cc_start: 0.7647 (p-80) cc_final: 0.7175 (p-80) REVERT: A 975 LEU cc_start: 0.8658 (mt) cc_final: 0.8198 (mt) REVERT: B 15 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7674 (t0) REVERT: B 62 TRP cc_start: 0.8014 (t60) cc_final: 0.7476 (t60) REVERT: B 67 GLU cc_start: 0.7814 (mp0) cc_final: 0.7519 (mp0) REVERT: B 84 VAL cc_start: 0.8184 (t) cc_final: 0.7599 (p) REVERT: B 85 VAL cc_start: 0.8669 (t) cc_final: 0.8415 (p) REVERT: B 92 MET cc_start: 0.8449 (mmm) cc_final: 0.8195 (mmm) REVERT: B 100 TYR cc_start: 0.7245 (t80) cc_final: 0.6381 (t80) REVERT: B 131 GLU cc_start: 0.7766 (tp30) cc_final: 0.7483 (tp30) REVERT: B 136 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7794 (mp0) REVERT: B 144 ASP cc_start: 0.8133 (m-30) cc_final: 0.7379 (m-30) REVERT: B 211 ASP cc_start: 0.7546 (t0) cc_final: 0.7185 (m-30) REVERT: B 237 ARG cc_start: 0.7398 (mtp85) cc_final: 0.6381 (mtp85) REVERT: B 299 LYS cc_start: 0.8095 (mmmm) cc_final: 0.7639 (mttp) REVERT: B 403 ASP cc_start: 0.7338 (m-30) cc_final: 0.6929 (m-30) REVERT: B 411 ASP cc_start: 0.7185 (t0) cc_final: 0.6904 (m-30) REVERT: B 412 GLU cc_start: 0.6809 (tt0) cc_final: 0.6412 (tt0) REVERT: B 492 ASP cc_start: 0.7935 (t0) cc_final: 0.7482 (t0) REVERT: B 544 ASN cc_start: 0.8421 (m-40) cc_final: 0.8173 (m-40) REVERT: B 585 TRP cc_start: 0.8669 (p-90) cc_final: 0.7827 (p-90) REVERT: B 599 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.6271 (pmt-80) REVERT: B 634 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8622 (mm110) REVERT: B 637 GLU cc_start: 0.7230 (tt0) cc_final: 0.6873 (tt0) REVERT: B 655 MET cc_start: 0.7876 (ttt) cc_final: 0.7561 (ttm) REVERT: B 667 GLU cc_start: 0.7180 (pm20) cc_final: 0.6891 (pm20) REVERT: B 672 VAL cc_start: 0.8471 (m) cc_final: 0.8254 (t) REVERT: B 677 LYS cc_start: 0.8445 (mtpt) cc_final: 0.7855 (mtpt) REVERT: B 693 GLN cc_start: 0.6923 (tp40) cc_final: 0.6083 (tp40) REVERT: B 708 TRP cc_start: 0.8300 (p-90) cc_final: 0.7756 (p-90) REVERT: B 905 ASN cc_start: 0.6876 (p0) cc_final: 0.6670 (p0) REVERT: B 919 ASP cc_start: 0.8111 (m-30) cc_final: 0.7404 (t0) REVERT: B 924 ASP cc_start: 0.8191 (m-30) cc_final: 0.7774 (p0) REVERT: B 983 TRP cc_start: 0.7958 (m100) cc_final: 0.7603 (m-10) REVERT: B 997 ASP cc_start: 0.7396 (m-30) cc_final: 0.6920 (t0) REVERT: B 1016 TYR cc_start: 0.7093 (p90) cc_final: 0.6821 (p90) REVERT: C 15 ASP cc_start: 0.8299 (m-30) cc_final: 0.7906 (t0) REVERT: C 43 ARG cc_start: 0.8601 (mtm110) cc_final: 0.8204 (mtm-85) REVERT: C 44 THR cc_start: 0.8916 (t) cc_final: 0.8689 (p) REVERT: C 62 TRP cc_start: 0.8174 (t60) cc_final: 0.7731 (t60) REVERT: C 84 VAL cc_start: 0.8212 (t) cc_final: 0.7688 (p) REVERT: C 85 VAL cc_start: 0.8770 (t) cc_final: 0.8479 (p) REVERT: C 92 MET cc_start: 0.8237 (mmm) cc_final: 0.7724 (mmm) REVERT: C 136 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7866 (mp0) REVERT: C 144 ASP cc_start: 0.7986 (m-30) cc_final: 0.7199 (m-30) REVERT: C 211 ASP cc_start: 0.7780 (t0) cc_final: 0.7270 (m-30) REVERT: C 237 ARG cc_start: 0.7408 (ttm-80) cc_final: 0.6981 (mtp85) REVERT: C 334 GLU cc_start: 0.6891 (tp30) cc_final: 0.6458 (tm-30) REVERT: C 349 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7453 (tp) REVERT: C 403 ASP cc_start: 0.7142 (m-30) cc_final: 0.6571 (m-30) REVERT: C 492 ASP cc_start: 0.7802 (t0) cc_final: 0.7442 (t0) REVERT: C 515 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8023 (m) REVERT: C 599 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.6189 (pmt-80) REVERT: C 634 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8533 (mm-40) REVERT: C 637 GLU cc_start: 0.7077 (tt0) cc_final: 0.6316 (tt0) REVERT: C 677 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7500 (mtpp) REVERT: C 693 GLN cc_start: 0.7261 (tp40) cc_final: 0.6749 (tp40) REVERT: C 708 TRP cc_start: 0.8340 (p-90) cc_final: 0.6952 (p-90) REVERT: C 744 GLU cc_start: 0.8269 (pm20) cc_final: 0.7881 (pm20) REVERT: C 757 GLN cc_start: 0.7655 (mt0) cc_final: 0.7207 (mt0) REVERT: C 761 GLN cc_start: 0.7048 (mm110) cc_final: 0.6758 (mp10) REVERT: C 792 ASP cc_start: 0.7790 (p0) cc_final: 0.7534 (p0) REVERT: C 808 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7486 (mm-30) REVERT: C 924 ASP cc_start: 0.8404 (m-30) cc_final: 0.8068 (t0) REVERT: C 945 ASN cc_start: 0.7653 (m-40) cc_final: 0.7389 (t0) REVERT: C 973 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7602 (ptm160) REVERT: C 997 ASP cc_start: 0.7146 (m-30) cc_final: 0.6759 (t0) REVERT: D 15 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7862 (t0) REVERT: D 62 TRP cc_start: 0.8113 (t60) cc_final: 0.7727 (t60) REVERT: D 67 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7452 (mp0) REVERT: D 75 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7387 (tm-30) REVERT: D 84 VAL cc_start: 0.8199 (t) cc_final: 0.7691 (p) REVERT: D 85 VAL cc_start: 0.8610 (t) cc_final: 0.8373 (p) REVERT: D 100 TYR cc_start: 0.7064 (t80) cc_final: 0.6243 (t80) REVERT: D 144 ASP cc_start: 0.8108 (m-30) cc_final: 0.7458 (m-30) REVERT: D 170 GLU cc_start: 0.6951 (pm20) cc_final: 0.6677 (pm20) REVERT: D 181 GLU cc_start: 0.8336 (pm20) cc_final: 0.8131 (pm20) REVERT: D 211 ASP cc_start: 0.7730 (t0) cc_final: 0.7349 (m-30) REVERT: D 241 GLU cc_start: 0.7073 (pt0) cc_final: 0.6789 (mt-10) REVERT: D 243 GLU cc_start: 0.6949 (tt0) cc_final: 0.6624 (tt0) REVERT: D 245 GLN cc_start: 0.7190 (tt0) cc_final: 0.6762 (mt0) REVERT: D 288 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7210 (mtt180) REVERT: D 403 ASP cc_start: 0.7405 (m-30) cc_final: 0.7042 (m-30) REVERT: D 492 ASP cc_start: 0.7803 (t0) cc_final: 0.7407 (t0) REVERT: D 599 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6599 (pmt-80) REVERT: D 634 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8546 (mm-40) REVERT: D 655 MET cc_start: 0.7808 (ttt) cc_final: 0.7582 (ttm) REVERT: D 677 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8006 (mtpp) REVERT: D 768 MET cc_start: 0.5608 (ttm) cc_final: 0.5088 (ttm) REVERT: D 773 LYS cc_start: 0.6333 (tmtt) cc_final: 0.6027 (tmtt) REVERT: D 819 GLU cc_start: 0.7469 (pm20) cc_final: 0.7239 (pm20) REVERT: D 874 SER cc_start: 0.9278 (m) cc_final: 0.8869 (p) REVERT: D 898 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6269 (tp) REVERT: D 924 ASP cc_start: 0.8295 (m-30) cc_final: 0.8012 (t0) REVERT: D 952 ARG cc_start: 0.7601 (ttm-80) cc_final: 0.7376 (ttm110) REVERT: D 973 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7436 (ptm160) REVERT: D 997 ASP cc_start: 0.7353 (m-30) cc_final: 0.6750 (t0) outliers start: 106 outliers final: 83 residues processed: 849 average time/residue: 0.4752 time to fit residues: 632.2048 Evaluate side-chains 876 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 779 time to evaluate : 3.269 ------------------------------------------------------------------------------- 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 181 GLU 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 687 GLN 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 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 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 323 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 379 MET 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 782 ASP Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 838 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 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 120 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 323 ILE 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 745 MET 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 973 ARG Chi-restraints excluded: chain C residue 984 LEU 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 120 THR Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 266 GLN 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 663 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 870 VAL Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 898 LEU Chi-restraints excluded: chain D residue 925 MET Chi-restraints excluded: chain D residue 959 ILE Chi-restraints excluded: chain D residue 973 ARG Chi-restraints excluded: chain D residue 984 LEU 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 43 optimal weight: 0.2980 chunk 259 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 404 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 114 optimal weight: 0.0070 chunk 381 optimal weight: 1.9990 chunk 250 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 108 optimal weight: 0.0970 chunk 269 optimal weight: 6.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 ** B 359 HIS ** 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** ** C 974 HIS ** 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 775 GLN D 840 HIS ** D 974 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 = 0.3492 r_free = 0.3492 target = 0.117574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099974 restraints weight = 57557.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103442 restraints weight = 26838.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105683 restraints weight = 15244.493| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 33792 Z= 0.107 Angle : 0.640 9.243 46104 Z= 0.324 Chirality : 0.044 0.194 4820 Planarity : 0.004 0.048 6088 Dihedral : 4.463 39.653 4477 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.63 % Allowed : 19.19 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.13), residues: 4080 helix: -1.31 (0.29), residues: 340 sheet: 0.41 (0.14), residues: 1400 loop : -2.12 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 90 HIS 0.014 0.001 HIS B 974 PHE 0.011 0.001 PHE A 784 TYR 0.020 0.001 TYR C 161 ARG 0.009 0.000 ARG A 800 Details of bonding type rmsd hydrogen bonds : bond 0.02929 ( 856) hydrogen bonds : angle 4.70208 ( 2448) covalent geometry : bond 0.00244 (33792) covalent geometry : angle 0.64050 (46104) ********************** 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 902 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 810 time to evaluate : 3.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8476 (mtm110) cc_final: 0.8078 (ttm-80) REVERT: A 62 TRP cc_start: 0.8093 (t60) cc_final: 0.7608 (t60) REVERT: A 67 GLU cc_start: 0.7767 (mp0) cc_final: 0.7547 (mp0) REVERT: A 75 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7168 (tm-30) REVERT: A 84 VAL cc_start: 0.8024 (t) cc_final: 0.7460 (p) REVERT: A 85 VAL cc_start: 0.8665 (t) cc_final: 0.8396 (p) REVERT: A 100 TYR cc_start: 0.7011 (t80) cc_final: 0.6129 (t80) REVERT: A 136 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7768 (mp0) REVERT: A 144 ASP cc_start: 0.7929 (m-30) cc_final: 0.7147 (m-30) REVERT: A 161 TYR cc_start: 0.7884 (t80) cc_final: 0.7493 (t80) REVERT: A 178 ARG cc_start: 0.7765 (ptt180) cc_final: 0.7500 (ptt180) REVERT: A 237 ARG cc_start: 0.7470 (mtp85) cc_final: 0.7160 (mtp85) REVERT: A 241 GLU cc_start: 0.7008 (pt0) cc_final: 0.6614 (mt-10) REVERT: A 243 GLU cc_start: 0.7060 (tt0) cc_final: 0.6796 (tt0) REVERT: A 245 GLN cc_start: 0.6658 (tp40) cc_final: 0.6389 (tp40) REVERT: A 255 ARG cc_start: 0.7732 (mpt-90) cc_final: 0.7280 (mmt90) REVERT: A 338 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7187 (tm-30) REVERT: A 492 ASP cc_start: 0.7834 (t0) cc_final: 0.7345 (t0) REVERT: A 585 TRP cc_start: 0.8784 (p-90) cc_final: 0.7965 (p-90) REVERT: A 599 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6583 (pmt-80) REVERT: A 634 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8492 (mm110) REVERT: A 637 GLU cc_start: 0.7374 (tt0) cc_final: 0.6757 (tt0) REVERT: A 655 MET cc_start: 0.7869 (ttt) cc_final: 0.7587 (ttm) REVERT: A 677 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7565 (mtpp) REVERT: A 687 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: A 693 GLN cc_start: 0.7202 (tp40) cc_final: 0.6835 (tp-100) REVERT: A 708 TRP cc_start: 0.8457 (p-90) cc_final: 0.8030 (p-90) REVERT: A 721 ARG cc_start: 0.7639 (ttm-80) cc_final: 0.7208 (mtp-110) REVERT: A 739 HIS cc_start: 0.7540 (t-90) cc_final: 0.7330 (t-90) REVERT: A 749 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.6776 (pt) REVERT: A 756 TRP cc_start: 0.7393 (m-90) cc_final: 0.6871 (m-90) REVERT: A 792 ASP cc_start: 0.7734 (p0) cc_final: 0.7481 (p0) REVERT: A 924 ASP cc_start: 0.8203 (m-30) cc_final: 0.7972 (p0) REVERT: A 935 ASN cc_start: 0.8908 (p0) cc_final: 0.8633 (p0) REVERT: A 945 ASN cc_start: 0.7410 (m-40) cc_final: 0.7158 (t0) REVERT: A 973 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7399 (ptm160) REVERT: A 974 HIS cc_start: 0.7634 (p-80) cc_final: 0.7163 (p-80) REVERT: A 975 LEU cc_start: 0.8640 (mt) cc_final: 0.8153 (mt) REVERT: B 62 TRP cc_start: 0.7952 (t60) cc_final: 0.7368 (t60) REVERT: B 67 GLU cc_start: 0.7797 (mp0) cc_final: 0.7492 (mp0) REVERT: B 84 VAL cc_start: 0.8104 (t) cc_final: 0.7514 (p) REVERT: B 85 VAL cc_start: 0.8641 (t) cc_final: 0.8393 (p) REVERT: B 92 MET cc_start: 0.8423 (mmm) cc_final: 0.8165 (mmm) REVERT: B 100 TYR cc_start: 0.7084 (t80) cc_final: 0.6301 (t80) REVERT: B 131 GLU cc_start: 0.7710 (tp30) cc_final: 0.7426 (tp30) REVERT: B 136 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7972 (mp0) REVERT: B 144 ASP cc_start: 0.8123 (m-30) cc_final: 0.7352 (m-30) REVERT: B 161 TYR cc_start: 0.7738 (t80) cc_final: 0.7448 (t80) REVERT: B 211 ASP cc_start: 0.7517 (t0) cc_final: 0.7135 (m-30) REVERT: B 403 ASP cc_start: 0.7317 (m-30) cc_final: 0.6877 (m-30) REVERT: B 411 ASP cc_start: 0.7092 (t0) cc_final: 0.6809 (m-30) REVERT: B 412 GLU cc_start: 0.6665 (tt0) cc_final: 0.6281 (tt0) REVERT: B 461 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7173 (mt-10) REVERT: B 492 ASP cc_start: 0.7886 (t0) cc_final: 0.7382 (t0) REVERT: B 544 ASN cc_start: 0.8446 (m-40) cc_final: 0.8192 (m-40) REVERT: B 585 TRP cc_start: 0.8644 (p-90) cc_final: 0.7891 (p-90) REVERT: B 599 ARG cc_start: 0.6446 (OUTLIER) cc_final: 0.6009 (ppt170) REVERT: B 634 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8609 (mm110) REVERT: B 637 GLU cc_start: 0.7253 (tt0) cc_final: 0.7018 (tt0) REVERT: B 655 MET cc_start: 0.7864 (ttt) cc_final: 0.7547 (ttm) REVERT: B 677 LYS cc_start: 0.8413 (mtpt) cc_final: 0.7736 (mtpp) REVERT: B 693 GLN cc_start: 0.6947 (tp40) cc_final: 0.6492 (tp-100) REVERT: B 708 TRP cc_start: 0.8367 (p-90) cc_final: 0.7788 (p-90) REVERT: B 721 ARG cc_start: 0.7380 (mtp-110) cc_final: 0.7139 (mtp-110) REVERT: B 739 HIS cc_start: 0.7589 (t-90) cc_final: 0.7313 (t-90) REVERT: B 744 GLU cc_start: 0.8556 (pm20) cc_final: 0.8183 (pm20) REVERT: B 924 ASP cc_start: 0.8169 (m-30) cc_final: 0.7509 (t0) REVERT: B 973 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7565 (ptm160) REVERT: B 997 ASP cc_start: 0.7437 (m-30) cc_final: 0.6938 (t0) REVERT: B 1016 TYR cc_start: 0.6873 (p90) cc_final: 0.6664 (p90) REVERT: C 15 ASP cc_start: 0.8284 (m-30) cc_final: 0.7892 (t0) REVERT: C 44 THR cc_start: 0.8773 (t) cc_final: 0.8484 (p) REVERT: C 46 ARG cc_start: 0.8445 (tpp80) cc_final: 0.8125 (tpp80) REVERT: C 62 TRP cc_start: 0.8066 (t60) cc_final: 0.7626 (t60) REVERT: C 74 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.6903 (mp) REVERT: C 84 VAL cc_start: 0.8124 (t) cc_final: 0.7567 (p) REVERT: C 85 VAL cc_start: 0.8743 (t) cc_final: 0.8441 (p) REVERT: C 92 MET cc_start: 0.8207 (mmm) cc_final: 0.7689 (mmm) REVERT: C 100 TYR cc_start: 0.7220 (t80) cc_final: 0.6283 (t80) REVERT: C 136 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7781 (mp0) REVERT: C 144 ASP cc_start: 0.7943 (m-30) cc_final: 0.7178 (m-30) REVERT: C 211 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7373 (m-30) REVERT: C 237 ARG cc_start: 0.7366 (ttm-80) cc_final: 0.7087 (mtp85) REVERT: C 241 GLU cc_start: 0.7135 (pt0) cc_final: 0.6925 (mt-10) REVERT: C 334 GLU cc_start: 0.6863 (tp30) cc_final: 0.6392 (tm-30) REVERT: C 349 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7456 (tp) REVERT: C 372 MET cc_start: 0.6982 (mtm) cc_final: 0.6764 (mtt) REVERT: C 403 ASP cc_start: 0.7129 (m-30) cc_final: 0.6548 (m-30) REVERT: C 492 ASP cc_start: 0.7736 (t0) cc_final: 0.7339 (t0) REVERT: C 515 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.7983 (m) REVERT: C 599 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.6049 (pmt-80) REVERT: C 634 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8506 (mm-40) REVERT: C 637 GLU cc_start: 0.7106 (tt0) cc_final: 0.6312 (tt0) REVERT: C 677 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7442 (mtpp) REVERT: C 693 GLN cc_start: 0.7246 (tp40) cc_final: 0.6697 (tp40) REVERT: C 708 TRP cc_start: 0.8360 (p-90) cc_final: 0.6952 (p-90) REVERT: C 721 ARG cc_start: 0.7862 (tpp80) cc_final: 0.7629 (tpp80) REVERT: C 757 GLN cc_start: 0.7635 (mt0) cc_final: 0.7197 (mt0) REVERT: C 761 GLN cc_start: 0.7004 (mm110) cc_final: 0.6757 (mp10) REVERT: C 790 ASP cc_start: 0.7350 (t0) cc_final: 0.7141 (t0) REVERT: C 792 ASP cc_start: 0.7817 (p0) cc_final: 0.7585 (p0) REVERT: C 808 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7459 (mm-30) REVERT: C 824 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7639 (tm-30) REVERT: C 924 ASP cc_start: 0.8361 (m-30) cc_final: 0.8076 (t0) REVERT: C 945 ASN cc_start: 0.7539 (m-40) cc_final: 0.7318 (t0) REVERT: C 973 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7422 (ptt180) REVERT: C 997 ASP cc_start: 0.7176 (m-30) cc_final: 0.6872 (t0) REVERT: D 62 TRP cc_start: 0.8012 (t60) cc_final: 0.7631 (t60) REVERT: D 67 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7405 (mp0) REVERT: D 75 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7363 (tm-30) REVERT: D 84 VAL cc_start: 0.8087 (t) cc_final: 0.7558 (p) REVERT: D 85 VAL cc_start: 0.8602 (t) cc_final: 0.8368 (p) REVERT: D 100 TYR cc_start: 0.7284 (t80) cc_final: 0.6597 (t80) REVERT: D 144 ASP cc_start: 0.8100 (m-30) cc_final: 0.7411 (m-30) REVERT: D 170 GLU cc_start: 0.6863 (pm20) cc_final: 0.6537 (pm20) REVERT: D 181 GLU cc_start: 0.8356 (pm20) cc_final: 0.8151 (pm20) REVERT: D 211 ASP cc_start: 0.7713 (t0) cc_final: 0.7337 (m-30) REVERT: D 237 ARG cc_start: 0.7591 (mtp85) cc_final: 0.7220 (mtp85) REVERT: D 241 GLU cc_start: 0.7026 (pt0) cc_final: 0.6753 (mt-10) REVERT: D 243 GLU cc_start: 0.6958 (tt0) cc_final: 0.6642 (tt0) REVERT: D 245 GLN cc_start: 0.7162 (tt0) cc_final: 0.6777 (mt0) REVERT: D 288 ARG cc_start: 0.7583 (mtt180) cc_final: 0.7275 (mtt180) REVERT: D 403 ASP cc_start: 0.7382 (m-30) cc_final: 0.6970 (m-30) REVERT: D 492 ASP cc_start: 0.7773 (t0) cc_final: 0.7349 (t0) REVERT: D 599 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6589 (pmt-80) REVERT: D 634 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8548 (mm-40) REVERT: D 655 MET cc_start: 0.7809 (ttt) cc_final: 0.7566 (ttm) REVERT: D 667 GLU cc_start: 0.7307 (pm20) cc_final: 0.6799 (pm20) REVERT: D 677 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7958 (mtpp) REVERT: D 739 HIS cc_start: 0.7417 (t-90) cc_final: 0.7088 (t-90) REVERT: D 761 GLN cc_start: 0.6988 (mp10) cc_final: 0.6599 (mp10) REVERT: D 768 MET cc_start: 0.5545 (ttm) cc_final: 0.5066 (ttm) REVERT: D 773 LYS cc_start: 0.6303 (tmtt) cc_final: 0.6100 (tmtt) REVERT: D 776 LEU cc_start: 0.8187 (pp) cc_final: 0.7816 (pp) REVERT: D 819 GLU cc_start: 0.7432 (pm20) cc_final: 0.7198 (pm20) REVERT: D 874 SER cc_start: 0.9240 (m) cc_final: 0.8835 (p) REVERT: D 924 ASP cc_start: 0.8244 (m-30) cc_final: 0.7851 (t0) REVERT: D 952 ARG cc_start: 0.7598 (ttm-80) cc_final: 0.7310 (ttm110) REVERT: D 961 ARG cc_start: 0.7727 (tpt-90) cc_final: 0.7514 (ttt90) REVERT: D 973 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7492 (ptm160) REVERT: D 997 ASP cc_start: 0.7418 (m-30) cc_final: 0.6764 (t0) outliers start: 92 outliers final: 71 residues processed: 858 average time/residue: 0.4849 time to fit residues: 652.4234 Evaluate side-chains 875 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 790 time to evaluate : 3.386 ------------------------------------------------------------------------------- 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 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 687 GLN Chi-restraints excluded: chain A residue 749 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 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 14 ARG 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 362 LEU 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 782 ASP 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 959 ILE Chi-restraints excluded: chain B residue 973 ARG 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 177 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 323 ILE 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 745 MET Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 838 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 973 ARG 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 120 THR 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 663 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 838 THR 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 973 ARG Chi-restraints excluded: chain D residue 984 LEU 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 95 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 296 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 393 optimal weight: 0.5980 chunk 185 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 163 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 HIS ** 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 604 ASN C 840 HIS C 890 GLN ** C 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 974 HIS ** 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 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 840 HIS ** D 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099621 restraints weight = 57698.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103039 restraints weight = 27114.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.105274 restraints weight = 15486.847| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33792 Z= 0.118 Angle : 0.649 8.979 46104 Z= 0.329 Chirality : 0.045 0.253 4820 Planarity : 0.004 0.043 6088 Dihedral : 4.463 38.840 4477 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.57 % Allowed : 19.65 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.13), residues: 4080 helix: -1.24 (0.29), residues: 340 sheet: 0.41 (0.14), residues: 1404 loop : -2.08 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 58 HIS 0.014 0.001 HIS B 974 PHE 0.010 0.001 PHE A 758 TYR 0.021 0.001 TYR C 161 ARG 0.010 0.000 ARG B 721 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 856) hydrogen bonds : angle 4.71304 ( 2448) covalent geometry : bond 0.00274 (33792) covalent geometry : angle 0.64885 (46104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12708.87 seconds wall clock time: 221 minutes 14.32 seconds (13274.32 seconds total)