Starting phenix.real_space_refine on Mon Aug 25 07:53:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i35_35144/08_2025/8i35_35144_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i35_35144/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8i35_35144/08_2025/8i35_35144_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i35_35144/08_2025/8i35_35144_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i35_35144/08_2025/8i35_35144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i35_35144/08_2025/8i35_35144.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.074 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: F, E, B, C, D Time building chain proxies: 4.16, per 1000 atoms: 0.16 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: 2.17 Conformation dependent library (CDL) restraints added in 972.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.24 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: 4.84 Time building geometry restraints manager: 2.69 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'E' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.780 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: 0.220 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.860 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.500 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (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 ARG 0.002 0.000 ARG C 37 TYR 0.015 0.002 TYR C 148 PHE 0.012 0.002 PHE C 161 TRP 0.008 0.001 TRP E 386 HIS 0.015 0.002 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00665 (25884) covalent geometry : angle 0.89436 (35064) hydrogen bonds : bond 0.20879 ( 756) hydrogen bonds : angle 7.40390 ( 2124) *********************** 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 : 0.867 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: 0.7253 time to fit residues: 173.4242 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 : 0.803 ------------------------------------------------------------------------------- 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.0170 overall best weight: 1.2024 ------------------------------------------------------------------------------- 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 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: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.108675 restraints weight = 36113.788| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.15 r_work: 0.3166 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 25884 Z= 0.129 Angle : 0.489 4.513 35064 Z= 0.263 Chirality : 0.045 0.160 3960 Planarity : 0.004 0.039 4470 Dihedral : 8.002 80.411 3506 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.19 % Favored : 92.62 % Rotamer: Outliers : 1.78 % Allowed : 19.64 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.15), residues: 3156 helix: 0.73 (0.17), residues: 1068 sheet: -1.01 (0.21), residues: 654 loop : -1.76 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 502 TYR 0.011 0.001 TYR D 148 PHE 0.011 0.001 PHE E 225 TRP 0.008 0.001 TRP F 402 HIS 0.007 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00298 (25884) covalent geometry : angle 0.48870 (35064) hydrogen bonds : bond 0.04037 ( 756) hydrogen bonds : angle 5.09299 ( 2124) *********************** 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 240 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 314 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8717 (m) REVERT: F 361 TYR cc_start: 0.8699 (m-80) cc_final: 0.8491 (m-80) REVERT: E 107 ASP cc_start: 0.8618 (t70) cc_final: 0.8414 (t70) REVERT: E 128 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8514 (tttp) REVERT: E 314 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8692 (m) REVERT: B 314 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8664 (m) REVERT: C 314 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8697 (m) REVERT: D 107 ASP cc_start: 0.8671 (t70) cc_final: 0.8461 (t70) REVERT: D 314 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8729 (m) REVERT: D 461 MET cc_start: 0.3420 (mtt) cc_final: 0.3192 (ttt) outliers start: 49 outliers final: 6 residues processed: 239 average time/residue: 0.5846 time to fit residues: 160.7759 Evaluate side-chains 179 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 F residue 314 VAL Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 314 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 98 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 76 optimal weight: 0.0770 chunk 42 optimal weight: 6.9990 chunk 269 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.4942 ------------------------------------------------------------------------------- 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 D 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.148592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109490 restraints weight = 36021.269| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.07 r_work: 0.3167 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 25884 Z= 0.150 Angle : 0.494 4.637 35064 Z= 0.265 Chirality : 0.045 0.161 3960 Planarity : 0.004 0.037 4470 Dihedral : 7.909 76.631 3498 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.92 % Favored : 91.89 % Rotamer: Outliers : 2.11 % Allowed : 19.97 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.15), residues: 3156 helix: 0.92 (0.17), residues: 1080 sheet: -0.88 (0.22), residues: 600 loop : -1.72 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 37 TYR 0.012 0.001 TYR A 148 PHE 0.012 0.001 PHE E 225 TRP 0.006 0.001 TRP B 386 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00353 (25884) covalent geometry : angle 0.49368 (35064) hydrogen bonds : bond 0.04177 ( 756) hydrogen bonds : angle 4.91291 ( 2124) *********************** 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 239 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 181 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6795 (mp) REVERT: E 128 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8583 (tttp) REVERT: E 314 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8771 (m) REVERT: B 107 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7961 (t70) REVERT: B 314 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8688 (m) REVERT: B 431 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6812 (mp) REVERT: C 314 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8771 (m) REVERT: D 314 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8781 (m) outliers start: 58 outliers final: 15 residues processed: 233 average time/residue: 0.6005 time to fit residues: 162.0026 Evaluate side-chains 192 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 431 ILE 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 314 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 329 ILE 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 C residue 314 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 427 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 242 optimal weight: 6.9990 chunk 309 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 272 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 304 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 D 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.152726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.112925 restraints weight = 36092.915| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.22 r_work: 0.3197 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1753 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= 0.120 Angle : 0.457 4.390 35064 Z= 0.245 Chirality : 0.044 0.148 3960 Planarity : 0.003 0.037 4470 Dihedral : 7.623 68.873 3498 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.57 % Favored : 92.24 % Rotamer: Outliers : 1.74 % Allowed : 20.52 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.15), residues: 3156 helix: 1.16 (0.17), residues: 1080 sheet: -0.93 (0.21), residues: 666 loop : -1.56 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 37 TYR 0.011 0.001 TYR A 148 PHE 0.009 0.001 PHE E 225 TRP 0.006 0.001 TRP F 402 HIS 0.004 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00279 (25884) covalent geometry : angle 0.45653 (35064) hydrogen bonds : bond 0.03565 ( 756) hydrogen bonds : angle 4.68745 ( 2124) *********************** 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 234 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 259 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: E 128 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8541 (tttp) REVERT: E 305 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8111 (mtpm) REVERT: B 107 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7935 (t70) REVERT: B 305 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7989 (mtpm) REVERT: C 314 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8711 (m) REVERT: D 305 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8131 (mtpm) outliers start: 48 outliers final: 19 residues processed: 226 average time/residue: 0.6200 time to fit residues: 161.4517 Evaluate side-chains 204 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 259 GLU 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 305 LYS Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 427 VAL 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 314 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 22 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 273 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 88 optimal weight: 0.0980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 F 260 GLN E 154 GLN C 154 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 = 0.3838 r_free = 0.3838 target = 0.148168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107529 restraints weight = 36116.797| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.19 r_work: 0.3153 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 25884 Z= 0.159 Angle : 0.490 4.743 35064 Z= 0.264 Chirality : 0.046 0.156 3960 Planarity : 0.003 0.038 4470 Dihedral : 7.660 59.887 3498 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.46 % Favored : 91.35 % Rotamer: Outliers : 2.18 % Allowed : 19.93 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.15), residues: 3156 helix: 1.18 (0.17), residues: 1080 sheet: -0.97 (0.21), residues: 666 loop : -1.54 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 49 TYR 0.012 0.001 TYR B 148 PHE 0.011 0.001 PHE D 225 TRP 0.006 0.001 TRP A 386 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00377 (25884) covalent geometry : angle 0.49040 (35064) hydrogen bonds : bond 0.04022 ( 756) hydrogen bonds : angle 4.71782 ( 2124) *********************** 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 230 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 170 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6840 (mp) REVERT: F 259 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: F 431 ILE cc_start: 0.7329 (OUTLIER) cc_final: 0.7102 (mp) REVERT: E 107 ASP cc_start: 0.8704 (t70) cc_final: 0.8494 (t70) REVERT: E 128 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8528 (tttp) REVERT: E 305 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8026 (mtpm) REVERT: E 314 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8746 (m) REVERT: B 305 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7891 (mtpm) REVERT: B 314 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8667 (m) REVERT: B 431 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6966 (mp) REVERT: C 305 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8049 (mtpm) REVERT: C 314 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8725 (m) REVERT: C 346 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: C 431 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6750 (mp) REVERT: D 107 ASP cc_start: 0.8676 (t70) cc_final: 0.8458 (t70) REVERT: D 305 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8052 (mtpm) REVERT: D 314 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8749 (m) REVERT: D 320 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6211 (ttt) REVERT: D 322 GLU cc_start: 0.8391 (mp0) cc_final: 0.8070 (mp0) outliers start: 60 outliers final: 23 residues processed: 222 average time/residue: 0.6257 time to fit residues: 159.4275 Evaluate side-chains 205 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR 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 76 TYR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 259 GLU 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 305 LYS Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 76 TYR 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 305 LYS Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 346 GLU 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 305 LYS Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 29 optimal weight: 0.0770 chunk 39 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 chunk 286 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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 D 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.152490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113005 restraints weight = 35955.713| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.14 r_work: 0.3201 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1924 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= 0.116 Angle : 0.451 4.406 35064 Z= 0.242 Chirality : 0.044 0.149 3960 Planarity : 0.003 0.037 4470 Dihedral : 7.386 59.497 3498 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.41 % Favored : 92.40 % Rotamer: Outliers : 1.82 % Allowed : 20.33 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.16), residues: 3156 helix: 1.35 (0.17), residues: 1080 sheet: -0.92 (0.21), residues: 666 loop : -1.48 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 37 TYR 0.011 0.001 TYR D 148 PHE 0.008 0.001 PHE E 225 TRP 0.005 0.001 TRP C 402 HIS 0.004 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00272 (25884) covalent geometry : angle 0.45135 (35064) hydrogen bonds : bond 0.03457 ( 756) hydrogen bonds : angle 4.56156 ( 2124) *********************** 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 230 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 259 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: E 128 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8557 (tttp) REVERT: E 305 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8105 (mtpm) REVERT: B 305 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7999 (mtpm) REVERT: B 314 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8668 (m) REVERT: C 314 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8708 (m) REVERT: C 431 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6938 (mp) REVERT: D 305 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8118 (mtpm) outliers start: 50 outliers final: 24 residues processed: 226 average time/residue: 0.5590 time to fit residues: 145.6547 Evaluate side-chains 209 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR 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 76 TYR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 259 GLU 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 305 LYS Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 76 TYR 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 314 VAL 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 305 LYS Chi-restraints excluded: chain D residue 427 VAL 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 214 optimal weight: 3.9990 chunk 63 optimal weight: 0.0470 chunk 291 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 216 optimal weight: 2.9990 chunk 305 optimal weight: 8.9990 chunk 283 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- 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 D 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.147710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107269 restraints weight = 35985.182| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.38 r_work: 0.3143 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 25884 Z= 0.172 Angle : 0.497 4.840 35064 Z= 0.267 Chirality : 0.046 0.157 3960 Planarity : 0.003 0.038 4470 Dihedral : 7.491 59.947 3498 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.75 % Favored : 91.06 % Rotamer: Outliers : 2.00 % Allowed : 20.15 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.16), residues: 3156 helix: 1.25 (0.17), residues: 1080 sheet: -0.99 (0.21), residues: 666 loop : -1.53 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 37 TYR 0.013 0.001 TYR D 174 PHE 0.011 0.001 PHE D 225 TRP 0.006 0.001 TRP E 386 HIS 0.006 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00410 (25884) covalent geometry : angle 0.49689 (35064) hydrogen bonds : bond 0.04056 ( 756) hydrogen bonds : angle 4.67192 ( 2124) *********************** 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 219 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 164 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6728 (mp) REVERT: F 259 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: F 305 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8011 (tttt) REVERT: E 128 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8574 (tttp) REVERT: E 305 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8039 (mtpm) REVERT: B 107 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7915 (t70) REVERT: B 305 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7896 (mtpm) REVERT: B 314 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8656 (m) REVERT: B 431 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6851 (mp) REVERT: C 314 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8731 (m) REVERT: C 346 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: C 431 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6833 (mp) REVERT: D 305 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8123 (mtpm) outliers start: 55 outliers final: 26 residues processed: 210 average time/residue: 0.6089 time to fit residues: 146.8219 Evaluate side-chains 197 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR 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 76 TYR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 305 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 305 LYS Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain B residue 62 LYS 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 314 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 431 ILE 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 314 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 427 VAL 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 178 optimal weight: 3.9990 chunk 20 optimal weight: 0.0060 chunk 161 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 300 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 223 optimal weight: 1.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN E 154 GLN B 260 GLN D 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.153215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113650 restraints weight = 35865.893| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.23 r_work: 0.3211 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2064 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= 0.093 Angle : 0.433 4.608 35064 Z= 0.232 Chirality : 0.044 0.142 3960 Planarity : 0.003 0.036 4470 Dihedral : 7.188 59.138 3498 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.88 % Favored : 92.93 % Rotamer: Outliers : 1.38 % Allowed : 20.95 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.16), residues: 3156 helix: 1.48 (0.17), residues: 1080 sheet: -0.89 (0.21), residues: 666 loop : -1.45 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 37 TYR 0.010 0.001 TYR C 148 PHE 0.007 0.001 PHE B 161 TRP 0.007 0.001 TRP E 290 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00216 (25884) covalent geometry : angle 0.43287 (35064) hydrogen bonds : bond 0.03158 ( 756) hydrogen bonds : angle 4.47387 ( 2124) *********************** 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 221 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6813 (mp) REVERT: F 259 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: F 305 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8002 (tttt) REVERT: E 128 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8541 (tttp) REVERT: E 305 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8145 (mtpm) REVERT: B 107 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7896 (t70) REVERT: B 305 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8006 (mtpm) REVERT: B 314 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8685 (m) REVERT: C 431 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6871 (mp) REVERT: D 305 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8214 (mtpm) REVERT: D 341 VAL cc_start: 0.7429 (t) cc_final: 0.7022 (p) outliers start: 38 outliers final: 17 residues processed: 216 average time/residue: 0.6056 time to fit residues: 150.6496 Evaluate side-chains 208 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR 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 76 TYR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 305 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 305 LYS Chi-restraints excluded: chain E residue 484 GLU 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 314 VAL 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 305 LYS Chi-restraints excluded: chain D residue 427 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 276 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 304 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 D 154 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.147005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106875 restraints weight = 36085.500| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.17 r_work: 0.3129 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 25884 Z= 0.204 Angle : 0.524 5.024 35064 Z= 0.280 Chirality : 0.047 0.160 3960 Planarity : 0.004 0.037 4470 Dihedral : 7.525 59.659 3498 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.00 % Favored : 90.81 % Rotamer: Outliers : 1.67 % Allowed : 21.21 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.15), residues: 3156 helix: 1.25 (0.17), residues: 1050 sheet: -1.03 (0.21), residues: 666 loop : -1.56 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 49 TYR 0.017 0.002 TYR D 174 PHE 0.012 0.002 PHE E 225 TRP 0.007 0.001 TRP E 386 HIS 0.006 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00491 (25884) covalent geometry : angle 0.52388 (35064) hydrogen bonds : bond 0.04304 ( 756) hydrogen bonds : angle 4.70157 ( 2124) *********************** 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 208 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.7138 (OUTLIER) cc_final: 0.6843 (mp) REVERT: F 259 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: F 305 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8050 (tttt) REVERT: E 128 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8603 (tttp) REVERT: E 305 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8084 (mtpm) REVERT: B 107 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7936 (t70) REVERT: B 314 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8658 (m) REVERT: C 346 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8277 (tt0) REVERT: C 431 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6933 (mp) REVERT: D 305 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8157 (mtpm) REVERT: D 322 GLU cc_start: 0.8420 (mp0) cc_final: 0.7914 (mp0) REVERT: D 341 VAL cc_start: 0.7395 (t) cc_final: 0.7065 (p) outliers start: 46 outliers final: 25 residues processed: 201 average time/residue: 0.6235 time to fit residues: 144.1275 Evaluate side-chains 193 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR 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 76 TYR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain E residue 86 ILE 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 E residue 427 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 427 VAL 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 346 GLU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 34 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 D 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.151342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112101 restraints weight = 35716.078| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.06 r_work: 0.3170 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 25884 Z= 0.151 Angle : 0.485 5.083 35064 Z= 0.260 Chirality : 0.045 0.159 3960 Planarity : 0.003 0.038 4470 Dihedral : 7.398 59.593 3498 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.24 % Favored : 91.57 % Rotamer: Outliers : 1.38 % Allowed : 21.64 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.16), residues: 3156 helix: 1.29 (0.17), residues: 1080 sheet: -1.03 (0.21), residues: 666 loop : -1.54 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 37 TYR 0.013 0.001 TYR D 174 PHE 0.010 0.001 PHE D 225 TRP 0.006 0.001 TRP A 386 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00358 (25884) covalent geometry : angle 0.48546 (35064) hydrogen bonds : bond 0.03791 ( 756) hydrogen bonds : angle 4.62360 ( 2124) ********************** 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 199 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6972 (mp) REVERT: F 259 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: E 128 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8617 (tttp) REVERT: E 305 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8215 (mtpm) REVERT: B 107 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.8003 (t70) REVERT: B 305 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8128 (mtpm) REVERT: B 314 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8698 (m) REVERT: C 346 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: C 431 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.7101 (mp) REVERT: D 305 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8283 (mtpm) REVERT: D 341 VAL cc_start: 0.7524 (t) cc_final: 0.7211 (p) outliers start: 38 outliers final: 24 residues processed: 195 average time/residue: 0.6830 time to fit residues: 152.7818 Evaluate side-chains 193 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR 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 76 TYR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain F residue 430 MET 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 E residue 427 VAL Chi-restraints excluded: chain E residue 484 GLU 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 314 VAL Chi-restraints excluded: chain B residue 427 VAL 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 346 GLU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 80 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 232 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 266 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- 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 D 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.150028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111635 restraints weight = 35305.020| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.04 r_work: 0.3185 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 25884 Z= 0.188 Angle : 0.519 5.562 35064 Z= 0.278 Chirality : 0.046 0.162 3960 Planarity : 0.004 0.038 4470 Dihedral : 7.533 59.334 3498 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.19 % Favored : 90.62 % Rotamer: Outliers : 1.53 % Allowed : 21.35 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.15), residues: 3156 helix: 1.18 (0.17), residues: 1080 sheet: -1.10 (0.21), residues: 666 loop : -1.59 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 49 TYR 0.016 0.002 TYR D 174 PHE 0.011 0.001 PHE D 225 TRP 0.007 0.001 TRP F 466 HIS 0.006 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00450 (25884) covalent geometry : angle 0.51862 (35064) hydrogen bonds : bond 0.04204 ( 756) hydrogen bonds : angle 4.71349 ( 2124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7904.31 seconds wall clock time: 135 minutes 32.71 seconds (8132.71 seconds total)