Starting phenix.real_space_refine on Sun Jun 22 19:43:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i35_35144/06_2025/8i35_35144_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i35_35144/06_2025/8i35_35144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i35_35144/06_2025/8i35_35144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i35_35144/06_2025/8i35_35144.map" model { file = "/net/cci-nas-00/data/ceres_data/8i35_35144/06_2025/8i35_35144_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i35_35144/06_2025/8i35_35144_neut_trim.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.074 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 S 108 5.16 5 C 16266 2.51 5 N 4224 2.21 5 O 4728 1.98 5 H 744 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26070 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4325 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 11.79, per 1000 atoms: 0.45 Number of scatterers: 26070 At special positions: 0 Unit cell: (169.338, 157.17, 94.302, 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 108 16.00 O 4728 8.00 N 4224 7.00 C 16266 6.00 H 744 1.00 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: 7.15 Conformation dependent library (CDL) restraints added in 3.3 seconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 24 sheets defined 37.9% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 3.578A pdb=" N LEU A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 58 Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.699A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix removed outlier: 3.548A pdb=" N GLY A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.611A pdb=" N GLN A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.693A pdb=" N GLN A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 250 through 262 removed outlier: 3.548A pdb=" N LEU A 255 " --> pdb=" O PRO A 251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.762A pdb=" N GLU A 338 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 339' Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 removed outlier: 3.632A pdb=" N TYR A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 440 through 449 removed outlier: 3.568A pdb=" N GLU A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 493 removed outlier: 3.557A pdb=" N ASP A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'F' and resid 15 through 21 removed outlier: 3.578A pdb=" N LEU F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 58 Processing helix chain 'F' and resid 73 through 87 removed outlier: 3.699A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix removed outlier: 3.548A pdb=" N GLY F 87 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 120 through 126 removed outlier: 3.611A pdb=" N GLN F 126 " --> pdb=" O PRO F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 131 Processing helix chain 'F' and resid 146 through 154 removed outlier: 3.692A pdb=" N GLN F 154 " --> pdb=" O ARG F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 204 Processing helix chain 'F' and resid 228 through 230 No H-bonds generated for 'chain 'F' and resid 228 through 230' Processing helix chain 'F' and resid 231 through 240 Processing helix chain 'F' and resid 250 through 262 removed outlier: 3.547A pdb=" N LEU F 255 " --> pdb=" O PRO F 251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN F 256 " --> pdb=" O ASP F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 281 through 285 Processing helix chain 'F' and resid 300 through 309 Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.763A pdb=" N GLU F 338 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 339 " --> pdb=" O GLN F 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 335 through 339' Processing helix chain 'F' and resid 340 through 349 Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 403 through 406 removed outlier: 3.632A pdb=" N TYR F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 403 through 406' Processing helix chain 'F' and resid 440 through 449 removed outlier: 3.567A pdb=" N GLU F 444 " --> pdb=" O SER F 440 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP F 445 " --> pdb=" O LEU F 441 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE F 446 " --> pdb=" O GLU F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 493 removed outlier: 3.557A pdb=" N ASP F 493 " --> pdb=" O GLY F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 533 Processing helix chain 'E' and resid 15 through 21 removed outlier: 3.577A pdb=" N LEU E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 58 Processing helix chain 'E' and resid 73 through 87 removed outlier: 3.699A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Proline residue: E 84 - end of helix removed outlier: 3.548A pdb=" N GLY E 87 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 120 through 126 removed outlier: 3.610A pdb=" N GLN E 126 " --> pdb=" O PRO E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.693A pdb=" N GLN E 154 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 250 through 262 removed outlier: 3.548A pdb=" N LEU E 255 " --> pdb=" O PRO E 251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN E 256 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 300 through 309 Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.762A pdb=" N GLU E 338 " --> pdb=" O GLU E 335 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 339 " --> pdb=" O GLN E 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 335 through 339' Processing helix chain 'E' and resid 340 through 349 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 403 through 406 removed outlier: 3.632A pdb=" N TYR E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 403 through 406' Processing helix chain 'E' and resid 440 through 449 removed outlier: 3.568A pdb=" N GLU E 444 " --> pdb=" O SER E 440 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE E 446 " --> pdb=" O GLU E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 493 removed outlier: 3.558A pdb=" N ASP E 493 " --> pdb=" O GLY E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 533 Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.578A pdb=" N LEU B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.700A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix removed outlier: 3.547A pdb=" N GLY B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.611A pdb=" N GLN B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.693A pdb=" N GLN B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 250 through 262 removed outlier: 3.548A pdb=" N LEU B 255 " --> pdb=" O PRO B 251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 300 through 309 Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.763A pdb=" N GLU B 338 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 335 through 339' Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.632A pdb=" N TYR B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 440 through 449 removed outlier: 3.568A pdb=" N GLU B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 493 removed outlier: 3.557A pdb=" N ASP B 493 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'C' and resid 15 through 21 removed outlier: 3.578A pdb=" N LEU C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 73 through 87 removed outlier: 3.699A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix removed outlier: 3.548A pdb=" N GLY C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.611A pdb=" N GLN C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 146 through 154 removed outlier: 3.692A pdb=" N GLN C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 250 through 262 removed outlier: 3.547A pdb=" N LEU C 255 " --> pdb=" O PRO C 251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.762A pdb=" N GLU C 338 " --> pdb=" O GLU C 335 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 339 " --> pdb=" O GLN C 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 335 through 339' Processing helix chain 'C' and resid 340 through 349 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 403 through 406 removed outlier: 3.632A pdb=" N TYR C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 406' Processing helix chain 'C' and resid 440 through 449 removed outlier: 3.568A pdb=" N GLU C 444 " --> pdb=" O SER C 440 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 446 " --> pdb=" O GLU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 493 removed outlier: 3.557A pdb=" N ASP C 493 " --> pdb=" O GLY C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 533 Processing helix chain 'D' and resid 15 through 21 removed outlier: 3.578A pdb=" N LEU D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 73 through 87 removed outlier: 3.699A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix removed outlier: 3.548A pdb=" N GLY D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 120 through 126 removed outlier: 3.610A pdb=" N GLN D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.692A pdb=" N GLN D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.547A pdb=" N LEU D 255 " --> pdb=" O PRO D 251 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 300 through 309 Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.762A pdb=" N GLU D 338 " --> pdb=" O GLU D 335 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 339 " --> pdb=" O GLN D 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 335 through 339' Processing helix chain 'D' and resid 340 through 349 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 403 through 406 removed outlier: 3.632A pdb=" N TYR D 406 " --> pdb=" O ARG D 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 403 through 406' Processing helix chain 'D' and resid 440 through 449 removed outlier: 3.568A pdb=" N GLU D 444 " --> pdb=" O SER D 440 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE D 446 " --> pdb=" O GLU D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 493 removed outlier: 3.557A pdb=" N ASP D 493 " --> pdb=" O GLY D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.740A pdb=" N GLU A 30 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR A 245 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 32 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER A 266 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 315 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 317 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 328 " --> pdb=" O TYR A 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.616A pdb=" N ILE A 114 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU A 140 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 116 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR A 65 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LEU A 115 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA A 67 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N HIS A 117 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N MET A 69 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 66 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU A 90 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 363 removed outlier: 5.427A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HIS A 414 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE A 423 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 461 removed outlier: 6.705A pdb=" N THR A 475 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A 456 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 473 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A 458 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 471 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY A 460 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL A 469 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N LYS A 510 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA A 472 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.740A pdb=" N GLU F 30 " --> pdb=" O GLN F 243 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR F 245 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL F 32 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE F 217 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N HIS F 267 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N MET F 219 " --> pdb=" O HIS F 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER F 266 " --> pdb=" O LYS F 291 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE F 315 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY F 317 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER F 328 " --> pdb=" O TYR F 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 136 through 140 removed outlier: 6.616A pdb=" N ILE F 114 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU F 140 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE F 116 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR F 65 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N LEU F 115 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA F 67 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N HIS F 117 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N MET F 69 " --> pdb=" O HIS F 117 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL F 66 " --> pdb=" O HIS F 91 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU F 90 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE F 187 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 361 through 363 removed outlier: 5.427A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HIS F 414 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE F 423 " --> pdb=" O HIS F 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 453 through 461 removed outlier: 6.705A pdb=" N THR F 475 " --> pdb=" O SER F 454 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL F 456 " --> pdb=" O LEU F 473 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU F 473 " --> pdb=" O VAL F 456 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL F 458 " --> pdb=" O LEU F 471 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU F 471 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY F 460 " --> pdb=" O VAL F 469 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL F 469 " --> pdb=" O GLY F 460 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N LYS F 510 " --> pdb=" O PRO F 470 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA F 472 " --> pdb=" O LYS F 510 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.739A pdb=" N GLU E 30 " --> pdb=" O GLN E 243 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR E 245 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL E 32 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE E 217 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N HIS E 267 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N MET E 219 " --> pdb=" O HIS E 267 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER E 266 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE E 315 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY E 317 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER E 328 " --> pdb=" O TYR E 318 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 136 through 140 removed outlier: 6.616A pdb=" N ILE E 114 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU E 140 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE E 116 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR E 65 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N LEU E 115 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA E 67 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N HIS E 117 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N MET E 69 " --> pdb=" O HIS E 117 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL E 66 " --> pdb=" O HIS E 91 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU E 90 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE E 187 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 361 through 363 removed outlier: 5.427A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N HIS E 414 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE E 423 " --> pdb=" O HIS E 414 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 453 through 461 removed outlier: 6.705A pdb=" N THR E 475 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL E 456 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU E 473 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL E 458 " --> pdb=" O LEU E 471 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU E 471 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY E 460 " --> pdb=" O VAL E 469 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL E 469 " --> pdb=" O GLY E 460 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N LYS E 510 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA E 472 " --> pdb=" O LYS E 510 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.740A pdb=" N GLU B 30 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N TYR B 245 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 32 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER B 266 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 315 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 317 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 328 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.616A pdb=" N ILE B 114 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU B 140 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 116 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B 65 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LEU B 115 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 67 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N HIS B 117 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N MET B 69 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 66 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 90 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 361 through 363 removed outlier: 5.427A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HIS B 414 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE B 423 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 453 through 461 removed outlier: 6.704A pdb=" N THR B 475 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B 456 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 473 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 458 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 471 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 460 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL B 469 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N LYS B 510 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA B 472 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.741A pdb=" N GLU C 30 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR C 245 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 32 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER C 266 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 315 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY C 317 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 328 " --> pdb=" O TYR C 318 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.616A pdb=" N ILE C 114 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU C 140 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE C 116 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR C 65 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LEU C 115 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA C 67 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N HIS C 117 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N MET C 69 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 66 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU C 90 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 361 through 363 removed outlier: 5.427A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HIS C 414 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE C 423 " --> pdb=" O HIS C 414 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 453 through 461 removed outlier: 6.706A pdb=" N THR C 475 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL C 456 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU C 473 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL C 458 " --> pdb=" O LEU C 471 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU C 471 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY C 460 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL C 469 " --> pdb=" O GLY C 460 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N LYS C 510 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA C 472 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.740A pdb=" N GLU D 30 " --> pdb=" O GLN D 243 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR D 245 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL D 32 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER D 266 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 315 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY D 317 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 328 " --> pdb=" O TYR D 318 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.615A pdb=" N ILE D 114 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU D 140 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE D 116 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR D 65 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N LEU D 115 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA D 67 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N HIS D 117 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N MET D 69 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL D 66 " --> pdb=" O HIS D 91 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU D 90 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 361 through 363 removed outlier: 5.427A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N HIS D 414 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE D 423 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 453 through 461 removed outlier: 6.704A pdb=" N THR D 475 " --> pdb=" O SER D 454 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL D 456 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU D 473 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL D 458 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU D 471 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY D 460 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL D 469 " --> pdb=" O GLY D 460 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N LYS D 510 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA D 472 " --> pdb=" O LYS D 510 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 2124 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: 9.90 Time building geometry restraints manager: 8.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 744 1.02 - 1.21: 75 1.21 - 1.41: 10425 1.41 - 1.61: 15192 1.61 - 1.81: 192 Bond restraints: 26628 Sorted by residual: bond pdb=" C10 OLA F1001 " pdb=" C9 OLA F1001 " ideal model delta sigma weight residual 1.332 1.519 -0.187 2.00e-02 2.50e+03 8.78e+01 bond pdb=" C10 OLA E1001 " pdb=" C9 OLA E1001 " ideal model delta sigma weight residual 1.332 1.519 -0.187 2.00e-02 2.50e+03 8.77e+01 bond pdb=" C10 OLA A1001 " pdb=" C9 OLA A1001 " ideal model delta sigma weight residual 1.332 1.519 -0.187 2.00e-02 2.50e+03 8.76e+01 bond pdb=" C10 OLA B1001 " pdb=" C9 OLA B1001 " ideal model delta sigma weight residual 1.332 1.519 -0.187 2.00e-02 2.50e+03 8.76e+01 bond pdb=" C10 OLA C1001 " pdb=" C9 OLA C1001 " ideal model delta sigma weight residual 1.332 1.519 -0.187 2.00e-02 2.50e+03 8.70e+01 ... (remaining 26623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 36031 2.91 - 5.82: 633 5.82 - 8.73: 68 8.73 - 11.65: 12 11.65 - 14.56: 12 Bond angle restraints: 36756 Sorted by residual: angle pdb=" N ILE F 433 " pdb=" CA ILE F 433 " pdb=" CB ILE F 433 " ideal model delta sigma weight residual 110.49 117.02 -6.53 1.15e+00 7.56e-01 3.23e+01 angle pdb=" N ILE E 433 " pdb=" CA ILE E 433 " pdb=" CB ILE E 433 " ideal model delta sigma weight residual 110.49 117.01 -6.52 1.15e+00 7.56e-01 3.22e+01 angle pdb=" N ILE C 433 " pdb=" CA ILE C 433 " pdb=" CB ILE C 433 " ideal model delta sigma weight residual 110.49 116.98 -6.49 1.15e+00 7.56e-01 3.19e+01 angle pdb=" N ILE A 433 " pdb=" CA ILE A 433 " pdb=" CB ILE A 433 " ideal model delta sigma weight residual 110.49 116.98 -6.49 1.15e+00 7.56e-01 3.19e+01 angle pdb=" N ILE B 433 " pdb=" CA ILE B 433 " pdb=" CB ILE B 433 " ideal model delta sigma weight residual 110.49 116.98 -6.49 1.15e+00 7.56e-01 3.19e+01 ... (remaining 36751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13643 17.97 - 35.95: 1567 35.95 - 53.92: 444 53.92 - 71.89: 84 71.89 - 89.86: 30 Dihedral angle restraints: 15768 sinusoidal: 6522 harmonic: 9246 Sorted by residual: dihedral pdb=" CA HIS C 532 " pdb=" C HIS C 532 " pdb=" N LEU C 533 " pdb=" CA LEU C 533 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA HIS F 532 " pdb=" C HIS F 532 " pdb=" N LEU F 533 " pdb=" CA LEU F 533 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA HIS B 532 " pdb=" C HIS B 532 " pdb=" N LEU B 533 " pdb=" CA LEU B 533 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 15765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3306 0.073 - 0.146: 577 0.146 - 0.219: 35 0.219 - 0.292: 24 0.292 - 0.365: 18 Chirality restraints: 3960 Sorted by residual: chirality pdb=" CA THR F 196 " pdb=" N THR F 196 " pdb=" C THR F 196 " pdb=" CB THR F 196 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA THR D 196 " pdb=" N THR D 196 " pdb=" C THR D 196 " pdb=" CB THR D 196 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA THR A 196 " pdb=" N THR A 196 " pdb=" C THR A 196 " pdb=" CB THR A 196 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3957 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA E1001 " 0.242 2.00e-02 2.50e+03 1.90e-01 3.62e+02 pdb=" C11 OLA E1001 " -0.117 2.00e-02 2.50e+03 pdb=" C8 OLA E1001 " 0.118 2.00e-02 2.50e+03 pdb=" C9 OLA E1001 " -0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA F1001 " -0.241 2.00e-02 2.50e+03 1.90e-01 3.62e+02 pdb=" C11 OLA F1001 " 0.117 2.00e-02 2.50e+03 pdb=" C8 OLA F1001 " -0.118 2.00e-02 2.50e+03 pdb=" C9 OLA F1001 " 0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA A1001 " 0.241 2.00e-02 2.50e+03 1.90e-01 3.62e+02 pdb=" C11 OLA A1001 " -0.117 2.00e-02 2.50e+03 pdb=" C8 OLA A1001 " 0.118 2.00e-02 2.50e+03 pdb=" C9 OLA A1001 " -0.243 2.00e-02 2.50e+03 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.39: 528 2.39 - 2.94: 13859 2.94 - 3.49: 31049 3.49 - 4.05: 52414 4.05 - 4.60: 78066 Nonbonded interactions: 175916 Sorted by model distance: nonbonded pdb=" HA ILE F 199 " pdb="HG22 THR F 202 " model vdw 1.834 2.440 nonbonded pdb=" HA ILE C 199 " pdb="HG22 THR C 202 " model vdw 1.834 2.440 nonbonded pdb=" HA ILE A 199 " pdb="HG22 THR A 202 " model vdw 1.835 2.440 nonbonded pdb=" HA ILE B 199 " pdb="HG22 THR B 202 " model vdw 1.835 2.440 nonbonded pdb=" HA ILE D 199 " pdb="HG22 THR D 202 " model vdw 1.835 2.440 ... (remaining 175911 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 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: 0.780 Extract box with map and model: 1.170 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 57.380 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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:15.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.007 0.187 25884 Z= 0.406 Angle : 0.894 14.556 35064 Z= 0.490 Chirality : 0.059 0.365 3960 Planarity : 0.009 0.190 4470 Dihedral : 16.847 89.863 9612 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.65 % Favored : 91.16 % Rotamer: Outliers : 0.29 % Allowed : 20.62 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 3156 helix: -0.12 (0.16), residues: 1068 sheet: -0.80 (0.22), residues: 558 loop : -1.70 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 386 HIS 0.015 0.002 HIS E 213 PHE 0.012 0.002 PHE C 161 TYR 0.015 0.002 TYR C 148 ARG 0.002 0.000 ARG C 37 Details of bonding type rmsd hydrogen bonds : bond 0.20879 ( 756) hydrogen bonds : angle 7.40390 ( 2124) covalent geometry : bond 0.00665 (25884) covalent geometry : angle 0.89436 (35064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 3.137 Fit side-chains REVERT: A 238 MET cc_start: 0.9220 (tpp) cc_final: 0.8439 (tpt) REVERT: A 399 LYS cc_start: 0.8955 (mtpm) cc_final: 0.8371 (mttp) REVERT: F 379 GLU cc_start: 0.8762 (tt0) cc_final: 0.8520 (tt0) REVERT: F 425 ASP cc_start: 0.7911 (t0) cc_final: 0.7616 (t0) REVERT: E 107 ASP cc_start: 0.8421 (t70) cc_final: 0.8172 (t70) REVERT: B 238 MET cc_start: 0.9191 (tpp) cc_final: 0.8424 (tpt) REVERT: C 425 ASP cc_start: 0.7968 (t0) cc_final: 0.7685 (t0) REVERT: D 107 ASP cc_start: 0.8443 (t70) cc_final: 0.8191 (t70) outliers start: 8 outliers final: 2 residues processed: 211 average time/residue: 1.7958 time to fit residues: 430.8051 Evaluate side-chains 172 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 3.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain B residue 128 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 0.0370 chunk 94 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 182 optimal weight: 3.9990 chunk 283 optimal weight: 0.6980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 29 GLN A 117 HIS A 154 GLN A 206 ASN A 213 HIS A 228 HIS A 267 HIS A 274 HIS A 408 HIS F 6 ASN F 12 GLN F 29 GLN F 117 HIS F 154 GLN F 206 ASN F 213 HIS F 228 HIS F 267 HIS F 274 HIS F 408 HIS E 12 GLN E 29 GLN E 117 HIS E 154 GLN E 206 ASN E 213 HIS E 228 HIS E 267 HIS E 274 HIS E 408 HIS B 12 GLN B 29 GLN B 117 HIS B 154 GLN B 206 ASN B 213 HIS B 228 HIS B 267 HIS B 274 HIS B 408 HIS C 12 GLN C 29 GLN C 117 HIS C 154 GLN C 206 ASN C 213 HIS C 228 HIS C 267 HIS C 274 HIS C 408 HIS D 12 GLN D 29 GLN D 117 HIS D 154 GLN D 206 ASN D 213 HIS D 228 HIS D 267 HIS D 274 HIS D 408 HIS Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.150610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.110513 restraints weight = 35970.300| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.17 r_work: 0.3196 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 25884 Z= 0.093 Angle : 0.456 4.164 35064 Z= 0.244 Chirality : 0.044 0.148 3960 Planarity : 0.003 0.037 4470 Dihedral : 7.947 81.017 3506 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.43 % Favored : 93.38 % Rotamer: Outliers : 1.63 % Allowed : 19.75 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 3156 helix: 0.78 (0.17), residues: 1074 sheet: -0.92 (0.21), residues: 648 loop : -1.73 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 290 HIS 0.005 0.001 HIS C 228 PHE 0.008 0.001 PHE E 225 TYR 0.009 0.001 TYR D 148 ARG 0.001 0.000 ARG C 502 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 756) hydrogen bonds : angle 5.05195 ( 2124) covalent geometry : bond 0.00208 (25884) covalent geometry : angle 0.45603 (35064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 3.010 Fit side-chains REVERT: E 107 ASP cc_start: 0.8602 (t70) cc_final: 0.8398 (t70) REVERT: E 128 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8455 (tttp) REVERT: E 281 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7927 (mtpm) REVERT: E 431 ILE cc_start: 0.6173 (mp) cc_final: 0.5970 (mp) REVERT: D 107 ASP cc_start: 0.8644 (t70) cc_final: 0.8436 (t70) REVERT: D 461 MET cc_start: 0.3376 (mtt) cc_final: 0.3165 (ttt) outliers start: 45 outliers final: 5 residues processed: 237 average time/residue: 1.5191 time to fit residues: 415.4022 Evaluate side-chains 178 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 171 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 207 optimal weight: 9.9990 chunk 298 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 185 optimal weight: 0.0670 chunk 192 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN F 154 GLN E 154 GLN E 206 ASN C 154 GLN D 206 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.154941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.115695 restraints weight = 36035.948| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.11 r_work: 0.3239 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 25884 Z= 0.087 Angle : 0.427 4.115 35064 Z= 0.228 Chirality : 0.043 0.136 3960 Planarity : 0.003 0.031 4470 Dihedral : 7.460 77.411 3498 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.91 % Favored : 92.90 % Rotamer: Outliers : 0.98 % Allowed : 20.62 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3156 helix: 1.24 (0.17), residues: 1074 sheet: -0.80 (0.21), residues: 666 loop : -1.57 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 402 HIS 0.004 0.001 HIS E 228 PHE 0.008 0.001 PHE E 225 TYR 0.010 0.001 TYR C 148 ARG 0.001 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 756) hydrogen bonds : angle 4.62614 ( 2124) covalent geometry : bond 0.00199 (25884) covalent geometry : angle 0.42736 (35064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 3.190 Fit side-chains REVERT: E 128 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8497 (tttp) REVERT: B 100 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: B 107 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7927 (t70) REVERT: D 320 MET cc_start: 0.6944 (ttt) cc_final: 0.6702 (ttt) outliers start: 27 outliers final: 3 residues processed: 223 average time/residue: 1.5253 time to fit residues: 391.6382 Evaluate side-chains 185 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain C residue 76 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 226 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 306 optimal weight: 0.0060 chunk 131 optimal weight: 0.1980 chunk 268 optimal weight: 6.9990 chunk 252 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN F 154 GLN E 154 GLN E 206 ASN C 154 GLN D 206 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.151030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112480 restraints weight = 36021.477| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.06 r_work: 0.3185 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25884 Z= 0.177 Angle : 0.517 5.155 35064 Z= 0.277 Chirality : 0.047 0.166 3960 Planarity : 0.004 0.034 4470 Dihedral : 8.004 69.424 3498 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.30 % Favored : 91.51 % Rotamer: Outliers : 2.14 % Allowed : 19.90 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 3156 helix: 1.09 (0.17), residues: 1080 sheet: -0.79 (0.22), residues: 600 loop : -1.63 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 290 HIS 0.007 0.001 HIS B 228 PHE 0.014 0.002 PHE E 225 TYR 0.013 0.002 TYR A 148 ARG 0.002 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 756) hydrogen bonds : angle 4.84621 ( 2124) covalent geometry : bond 0.00422 (25884) covalent geometry : angle 0.51656 (35064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 171 time to evaluate : 2.843 Fit side-chains revert: symmetry clash REVERT: A 431 ILE cc_start: 0.7304 (OUTLIER) cc_final: 0.6958 (mp) REVERT: F 62 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8058 (ttpt) REVERT: E 128 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8645 (tttp) REVERT: E 305 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8192 (mtpm) REVERT: B 107 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7975 (t70) REVERT: B 281 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8229 (mtpm) REVERT: B 305 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8075 (mtpm) REVERT: B 431 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.7008 (mp) REVERT: C 62 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8073 (ttpt) REVERT: D 305 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8207 (mtpm) outliers start: 59 outliers final: 13 residues processed: 219 average time/residue: 1.4795 time to fit residues: 373.2905 Evaluate side-chains 189 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 305 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 27 optimal weight: 0.0040 chunk 162 optimal weight: 7.9990 chunk 29 optimal weight: 0.0470 chunk 294 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 255 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 overall best weight: 0.4290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN F 154 GLN E 154 GLN C 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.156047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116916 restraints weight = 36181.635| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.25 r_work: 0.3253 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 25884 Z= 0.068 Angle : 0.403 3.688 35064 Z= 0.214 Chirality : 0.043 0.133 3960 Planarity : 0.003 0.032 4470 Dihedral : 7.246 60.788 3498 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.05 % Favored : 93.76 % Rotamer: Outliers : 1.09 % Allowed : 20.62 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 3156 helix: 1.54 (0.17), residues: 1074 sheet: -0.69 (0.22), residues: 648 loop : -1.39 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 290 HIS 0.003 0.001 HIS B 39 PHE 0.006 0.001 PHE A 173 TYR 0.007 0.001 TYR F 148 ARG 0.001 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.02677 ( 756) hydrogen bonds : angle 4.42940 ( 2124) covalent geometry : bond 0.00151 (25884) covalent geometry : angle 0.40263 (35064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 3.566 Fit side-chains REVERT: A 431 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6824 (mp) REVERT: F 305 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8062 (tttt) REVERT: E 107 ASP cc_start: 0.8646 (t70) cc_final: 0.8437 (t70) REVERT: E 128 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8483 (tttp) REVERT: B 37 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7867 (ttm110) REVERT: B 305 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8033 (mtpm) outliers start: 30 outliers final: 7 residues processed: 227 average time/residue: 2.0217 time to fit residues: 534.6141 Evaluate side-chains 202 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 18 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 136 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 311 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN F 154 GLN E 154 GLN ** E 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.152622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.113371 restraints weight = 35941.024| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.18 r_work: 0.3184 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 25884 Z= 0.129 Angle : 0.459 4.394 35064 Z= 0.245 Chirality : 0.044 0.137 3960 Planarity : 0.003 0.032 4470 Dihedral : 7.426 59.814 3498 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.73 % Favored : 92.08 % Rotamer: Outliers : 1.34 % Allowed : 20.88 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 3156 helix: 1.51 (0.17), residues: 1080 sheet: -0.70 (0.21), residues: 666 loop : -1.37 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 290 HIS 0.006 0.001 HIS A 228 PHE 0.011 0.001 PHE E 225 TYR 0.012 0.001 TYR B 148 ARG 0.002 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 756) hydrogen bonds : angle 4.52313 ( 2124) covalent geometry : bond 0.00303 (25884) covalent geometry : angle 0.45854 (35064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 4.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7039 (mp) REVERT: E 128 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8611 (tttp) REVERT: E 228 HIS cc_start: 0.8972 (m170) cc_final: 0.8732 (m90) REVERT: E 431 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6544 (mp) REVERT: B 107 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.8006 (t70) REVERT: B 305 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8135 (mtpm) REVERT: B 431 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.7017 (mp) REVERT: D 431 ILE cc_start: 0.7108 (OUTLIER) cc_final: 0.6556 (mp) outliers start: 37 outliers final: 17 residues processed: 210 average time/residue: 1.5056 time to fit residues: 368.5182 Evaluate side-chains 200 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 19 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 238 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 269 optimal weight: 0.0020 chunk 287 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 259 optimal weight: 20.0000 chunk 303 optimal weight: 5.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN F 154 GLN E 154 GLN ** E 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.152914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113744 restraints weight = 35874.372| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.10 r_work: 0.3204 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 25884 Z= 0.121 Angle : 0.451 4.527 35064 Z= 0.241 Chirality : 0.044 0.151 3960 Planarity : 0.003 0.033 4470 Dihedral : 7.120 59.515 3498 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.45 % Favored : 92.36 % Rotamer: Outliers : 1.60 % Allowed : 20.77 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 3156 helix: 1.56 (0.17), residues: 1080 sheet: -0.69 (0.21), residues: 666 loop : -1.35 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 386 HIS 0.004 0.001 HIS E 39 PHE 0.009 0.001 PHE D 225 TYR 0.011 0.001 TYR D 148 ARG 0.001 0.000 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 756) hydrogen bonds : angle 4.48817 ( 2124) covalent geometry : bond 0.00284 (25884) covalent geometry : angle 0.45121 (35064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6854 (mp) REVERT: F 62 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8029 (ttpt) REVERT: E 128 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8577 (tttp) REVERT: E 228 HIS cc_start: 0.8929 (m170) cc_final: 0.8680 (m90) REVERT: E 431 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6407 (mp) REVERT: B 107 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7979 (t70) REVERT: B 305 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8108 (mtpm) REVERT: C 62 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7979 (ttpt) REVERT: D 431 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6465 (mp) outliers start: 44 outliers final: 21 residues processed: 217 average time/residue: 1.5112 time to fit residues: 379.0639 Evaluate side-chains 204 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 4.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 150 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 265 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 191 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 260 GLN F 154 GLN E 154 GLN E 228 HIS B 260 GLN C 154 GLN C 260 GLN D 154 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.146287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107102 restraints weight = 35896.353| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.14 r_work: 0.3126 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 25884 Z= 0.244 Angle : 0.562 5.294 35064 Z= 0.301 Chirality : 0.048 0.175 3960 Planarity : 0.004 0.034 4470 Dihedral : 7.449 59.234 3498 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.97 % Favored : 90.84 % Rotamer: Outliers : 1.78 % Allowed : 20.62 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3156 helix: 1.21 (0.17), residues: 1050 sheet: -0.90 (0.22), residues: 600 loop : -1.53 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 290 HIS 0.007 0.001 HIS F 228 PHE 0.014 0.002 PHE E 225 TYR 0.016 0.002 TYR A 174 ARG 0.004 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 756) hydrogen bonds : angle 4.80398 ( 2124) covalent geometry : bond 0.00589 (25884) covalent geometry : angle 0.56207 (35064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 165 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6782 (mp) REVERT: F 62 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7920 (ttpt) REVERT: F 431 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6982 (mp) REVERT: E 128 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8630 (tttp) REVERT: E 431 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6357 (mp) REVERT: B 107 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7939 (t70) REVERT: C 62 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7943 (ttpt) REVERT: C 431 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6723 (mp) REVERT: D 431 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6441 (mp) outliers start: 49 outliers final: 22 residues processed: 202 average time/residue: 1.4739 time to fit residues: 344.7889 Evaluate side-chains 191 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 231 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 43 optimal weight: 0.0470 chunk 276 optimal weight: 3.9990 chunk 252 optimal weight: 0.0980 chunk 196 optimal weight: 5.9990 chunk 261 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 260 GLN F 154 GLN E 154 GLN B 260 GLN C 260 GLN D 154 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.154025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114359 restraints weight = 35998.128| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.09 r_work: 0.3211 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 25884 Z= 0.087 Angle : 0.427 4.428 35064 Z= 0.228 Chirality : 0.044 0.147 3960 Planarity : 0.003 0.035 4470 Dihedral : 6.730 59.996 3498 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.40 % Favored : 93.41 % Rotamer: Outliers : 1.13 % Allowed : 21.31 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 3156 helix: 1.56 (0.17), residues: 1080 sheet: -0.74 (0.21), residues: 654 loop : -1.38 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 290 HIS 0.003 0.001 HIS D 39 PHE 0.008 0.001 PHE E 161 TYR 0.010 0.001 TYR F 148 ARG 0.001 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.03015 ( 756) hydrogen bonds : angle 4.46802 ( 2124) covalent geometry : bond 0.00202 (25884) covalent geometry : angle 0.42697 (35064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 62 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7958 (ttpt) REVERT: E 128 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8513 (tttp) REVERT: E 431 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6457 (mp) REVERT: B 107 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7944 (t70) REVERT: B 305 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8017 (mtpm) REVERT: C 62 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7946 (ttpt) REVERT: D 341 VAL cc_start: 0.7421 (t) cc_final: 0.7006 (p) REVERT: D 431 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6469 (mp) outliers start: 31 outliers final: 19 residues processed: 203 average time/residue: 1.3819 time to fit residues: 326.6918 Evaluate side-chains 198 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 431 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 174 optimal weight: 1.9990 chunk 276 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 251 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 260 GLN F 154 GLN E 154 GLN B 260 GLN C 260 GLN D 154 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.145948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106527 restraints weight = 35903.151| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.01 r_work: 0.3118 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 25884 Z= 0.275 Angle : 0.589 5.439 35064 Z= 0.313 Chirality : 0.049 0.172 3960 Planarity : 0.004 0.035 4470 Dihedral : 7.354 59.993 3498 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.09 % Favored : 90.72 % Rotamer: Outliers : 1.16 % Allowed : 21.46 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 3156 helix: 1.20 (0.17), residues: 1044 sheet: -1.00 (0.21), residues: 666 loop : -1.54 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 290 HIS 0.008 0.002 HIS F 228 PHE 0.015 0.002 PHE D 225 TYR 0.022 0.002 TYR D 174 ARG 0.004 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.04893 ( 756) hydrogen bonds : angle 4.83437 ( 2124) covalent geometry : bond 0.00667 (25884) covalent geometry : angle 0.58918 (35064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 62 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8037 (ttpt) REVERT: E 128 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8693 (tttp) REVERT: E 431 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6470 (mp) REVERT: B 107 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.8013 (t70) REVERT: B 305 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8012 (mtpm) outliers start: 32 outliers final: 20 residues processed: 188 average time/residue: 1.7080 time to fit residues: 372.6793 Evaluate side-chains 183 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 431 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 207 optimal weight: 20.0000 chunk 43 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 303 optimal weight: 9.9990 chunk 311 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 260 GLN E 154 GLN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.153789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.114125 restraints weight = 35768.702| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.07 r_work: 0.3214 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25884 Z= 0.088 Angle : 0.434 5.201 35064 Z= 0.231 Chirality : 0.044 0.148 3960 Planarity : 0.003 0.035 4470 Dihedral : 6.723 59.606 3498 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.53 % Favored : 93.28 % Rotamer: Outliers : 0.84 % Allowed : 21.93 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 3156 helix: 1.55 (0.17), residues: 1080 sheet: -0.75 (0.21), residues: 654 loop : -1.41 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 290 HIS 0.003 0.001 HIS C 228 PHE 0.008 0.001 PHE E 161 TYR 0.010 0.001 TYR C 148 ARG 0.001 0.000 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.03040 ( 756) hydrogen bonds : angle 4.47053 ( 2124) covalent geometry : bond 0.00204 (25884) covalent geometry : angle 0.43393 (35064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18612.60 seconds wall clock time: 324 minutes 32.12 seconds (19472.12 seconds total)