Starting phenix.real_space_refine on Tue Nov 19 02:40:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i49_35165/11_2024/8i49_35165_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i49_35165/11_2024/8i49_35165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i49_35165/11_2024/8i49_35165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i49_35165/11_2024/8i49_35165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i49_35165/11_2024/8i49_35165_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i49_35165/11_2024/8i49_35165_trim.cif" } resolution = 2.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.112 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 S 108 5.16 5 C 16302 2.51 5 N 4266 2.21 5 O 4812 1.98 5 H 25248 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 50754 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 8428 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 22.09, per 1000 atoms: 0.44 Number of scatterers: 50754 At special positions: 0 Unit cell: (169.338, 158.184, 96.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 18 15.00 O 4812 8.00 N 4266 7.00 C 16302 6.00 H 25248 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: 10.87 Conformation dependent library (CDL) restraints added in 3.0 seconds 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 30 sheets defined 38.3% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 removed outlier: 3.654A pdb=" N LEU A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 58 Processing helix chain 'A' and resid 73 through 86 removed outlier: 3.681A 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 Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.984A 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: 3.716A pdb=" N GLN A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 205 removed outlier: 3.856A pdb=" N THR A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.996A pdb=" N ALA A 284 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET A 285 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.620A pdb=" N LEU A 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) 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: 3.806A 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 439 through 449 removed outlier: 3.879A pdb=" N LEU A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 removed outlier: 4.353A pdb=" N PHE A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'D' and resid 14 through 21 removed outlier: 3.655A pdb=" N LEU D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 73 through 86 removed outlier: 3.681A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 120 through 126 removed outlier: 3.984A 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: 3.716A pdb=" N GLN D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.856A pdb=" N THR D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.996A pdb=" N ALA D 284 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET D 285 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 309 Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.620A pdb=" N LEU D 339 " --> pdb=" O GLN D 336 " (cutoff:3.500A) 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: 3.805A 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 439 through 449 removed outlier: 3.878A pdb=" N LEU D 443 " --> pdb=" O SER D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 494 removed outlier: 4.354A pdb=" N PHE D 494 " --> pdb=" O PHE D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 532 Processing helix chain 'E' and resid 14 through 21 removed outlier: 3.654A pdb=" N LEU E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 58 Processing helix chain 'E' and resid 73 through 86 removed outlier: 3.681A 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 Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 120 through 126 removed outlier: 3.984A 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: 3.716A pdb=" N GLN E 154 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 205 removed outlier: 3.857A pdb=" N THR E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 285 removed outlier: 3.996A pdb=" N ALA E 284 " --> pdb=" O LYS E 281 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET E 285 " --> pdb=" O SER E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 309 Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.620A pdb=" N LEU E 339 " --> pdb=" O GLN E 336 " (cutoff:3.500A) 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: 3.805A 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 439 through 449 removed outlier: 3.879A pdb=" N LEU E 443 " --> pdb=" O SER E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 494 removed outlier: 4.354A pdb=" N PHE E 494 " --> pdb=" O PHE E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 532 Processing helix chain 'F' and resid 14 through 21 removed outlier: 3.654A pdb=" N LEU F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 58 Processing helix chain 'F' and resid 73 through 86 removed outlier: 3.680A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 120 through 126 removed outlier: 3.985A 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: 3.717A pdb=" N GLN F 154 " --> pdb=" O ARG F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 205 removed outlier: 3.856A pdb=" N THR F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) 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 Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 280 through 285 removed outlier: 3.996A pdb=" N ALA F 284 " --> pdb=" O LYS F 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET F 285 " --> pdb=" O SER F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 309 Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.620A pdb=" N LEU F 339 " --> pdb=" O GLN F 336 " (cutoff:3.500A) 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: 3.806A 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 439 through 449 removed outlier: 3.880A pdb=" N LEU F 443 " --> pdb=" O SER F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 494 removed outlier: 4.354A pdb=" N PHE F 494 " --> pdb=" O PHE F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 532 Processing helix chain 'C' and resid 14 through 21 removed outlier: 3.655A pdb=" N LEU C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 73 through 86 removed outlier: 3.680A 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 Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.984A 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: 3.717A pdb=" N GLN C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 205 removed outlier: 3.856A pdb=" N THR C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.996A pdb=" N ALA C 284 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C 285 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.619A pdb=" N LEU C 339 " --> pdb=" O GLN C 336 " (cutoff:3.500A) 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: 3.806A 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 439 through 449 removed outlier: 3.879A pdb=" N LEU C 443 " --> pdb=" O SER C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 494 removed outlier: 4.353A pdb=" N PHE C 494 " --> pdb=" O PHE C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'B' and resid 14 through 21 removed outlier: 3.655A pdb=" N LEU B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 Processing helix chain 'B' and resid 73 through 86 removed outlier: 3.681A 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 Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.984A 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: 3.717A pdb=" N GLN B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.856A pdb=" N THR B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.996A pdb=" N ALA B 284 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.619A pdb=" N LEU B 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) 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: 3.805A 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 439 through 449 removed outlier: 3.879A pdb=" N LEU B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 494 removed outlier: 4.353A pdb=" N PHE B 494 " --> pdb=" O PHE B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.787A pdb=" N GLU A 30 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR A 245 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 32 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR A 218 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.982A pdb=" N THR A 65 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N LEU A 115 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA A 67 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N HIS A 117 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N MET A 69 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 66 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR A 174 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR A 172 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 185 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A 174 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LYS A 183 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 268 removed outlier: 6.791A pdb=" N SER A 266 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA A 316 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE A 329 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR A 318 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 361 through 363 removed outlier: 5.307A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLY A 410 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG A 426 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 412 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 461 removed outlier: 3.543A pdb=" N GLU A 455 " --> pdb=" O THR A 475 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.787A pdb=" N GLU D 30 " --> pdb=" O GLN D 243 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TYR D 245 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL D 32 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR D 218 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.982A pdb=" N THR D 65 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU D 115 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA D 67 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N HIS D 117 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N MET D 69 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL D 66 " --> pdb=" O HIS D 91 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR D 174 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR D 172 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL D 185 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR D 174 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LYS D 183 " --> pdb=" O TYR D 174 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 266 through 268 removed outlier: 6.792A pdb=" N SER D 266 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA D 316 " --> pdb=" O ILE D 329 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE D 329 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR D 318 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 361 through 363 removed outlier: 5.306A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N GLY D 410 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG D 426 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL D 412 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 453 through 461 removed outlier: 3.543A pdb=" N GLU D 455 " --> pdb=" O THR D 475 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.787A pdb=" N GLU E 30 " --> pdb=" O GLN E 243 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR E 245 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL E 32 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR E 218 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 136 through 140 removed outlier: 6.982A pdb=" N THR E 65 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N LEU E 115 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA E 67 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N HIS E 117 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N MET E 69 " --> pdb=" O HIS E 117 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL E 66 " --> pdb=" O HIS E 91 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR E 174 " --> pdb=" O MET E 92 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE E 187 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR E 172 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL E 185 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR E 174 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LYS E 183 " --> pdb=" O TYR E 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 266 through 268 removed outlier: 6.792A pdb=" N SER E 266 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA E 316 " --> pdb=" O ILE E 329 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE E 329 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR E 318 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 361 through 363 removed outlier: 5.307A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N GLY E 410 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG E 426 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL E 412 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 453 through 461 removed outlier: 3.542A pdb=" N GLU E 455 " --> pdb=" O THR E 475 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.787A pdb=" N GLU F 30 " --> pdb=" O GLN F 243 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TYR F 245 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL F 32 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR F 218 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 136 through 140 removed outlier: 6.981A pdb=" N THR F 65 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU F 115 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA F 67 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N HIS F 117 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N MET F 69 " --> pdb=" O HIS F 117 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL F 66 " --> pdb=" O HIS F 91 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR F 174 " --> pdb=" O MET F 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 266 through 268 removed outlier: 6.791A pdb=" N SER F 266 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA F 316 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE F 329 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR F 318 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 361 through 363 removed outlier: 5.307A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLY F 410 " --> pdb=" O ARG F 426 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG F 426 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL F 412 " --> pdb=" O THR F 424 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 453 through 461 removed outlier: 3.543A pdb=" N GLU F 455 " --> pdb=" O THR F 475 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.787A pdb=" N GLU C 30 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR C 245 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C 32 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR C 218 " --> pdb=" O VAL C 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.982A pdb=" N THR C 65 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N LEU C 115 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA C 67 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N HIS C 117 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N MET C 69 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL C 66 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR C 174 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR C 172 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 185 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR C 174 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS C 183 " --> pdb=" O TYR C 174 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 266 through 268 removed outlier: 6.791A pdb=" N SER C 266 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA C 316 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE C 329 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR C 318 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 361 through 363 removed outlier: 5.306A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLY C 410 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG C 426 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 412 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 453 through 461 removed outlier: 3.543A pdb=" N GLU C 455 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.787A pdb=" N GLU B 30 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TYR B 245 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 32 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR B 218 " --> pdb=" O VAL B 244 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.982A pdb=" N THR B 65 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N LEU B 115 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 67 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N HIS B 117 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N MET B 69 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 66 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR B 174 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 172 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 185 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR B 174 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LYS B 183 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 266 through 268 removed outlier: 6.792A pdb=" N SER B 266 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA B 316 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE B 329 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 318 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 363 removed outlier: 5.307A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N GLY B 410 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG B 426 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 412 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 453 through 461 removed outlier: 3.543A pdb=" N GLU B 455 " --> pdb=" O THR B 475 " (cutoff:3.500A) 881 hydrogen bonds defined for protein. 2442 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: 19.37 Time building geometry restraints manager: 13.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.01: 25224 1.01 - 1.21: 381 1.21 - 1.41: 10372 1.41 - 1.61: 15131 1.61 - 1.81: 228 Bond restraints: 51336 Sorted by residual: bond pdb=" C6 ATP D1101 " pdb=" N6 ATP D1101 " ideal model delta sigma weight residual 1.337 1.466 -0.129 1.10e-02 8.26e+03 1.37e+02 bond pdb=" C6 ATP B1101 " pdb=" N6 ATP B1101 " ideal model delta sigma weight residual 1.337 1.466 -0.129 1.10e-02 8.26e+03 1.37e+02 bond pdb=" C6 ATP A1101 " pdb=" N6 ATP A1101 " ideal model delta sigma weight residual 1.337 1.465 -0.128 1.10e-02 8.26e+03 1.36e+02 bond pdb=" C6 ATP C1101 " pdb=" N6 ATP C1101 " ideal model delta sigma weight residual 1.337 1.465 -0.128 1.10e-02 8.26e+03 1.36e+02 bond pdb=" C6 ATP E1101 " pdb=" N6 ATP E1101 " ideal model delta sigma weight residual 1.337 1.465 -0.128 1.10e-02 8.26e+03 1.36e+02 ... (remaining 51331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 86771 2.96 - 5.92: 5701 5.92 - 8.89: 486 8.89 - 11.85: 72 11.85 - 14.81: 30 Bond angle restraints: 93060 Sorted by residual: angle pdb=" PB ATP B1101 " pdb=" O3B ATP B1101 " pdb=" PG ATP B1101 " ideal model delta sigma weight residual 139.87 125.06 14.81 1.00e+00 1.00e+00 2.19e+02 angle pdb=" PB ATP D1101 " pdb=" O3B ATP D1101 " pdb=" PG ATP D1101 " ideal model delta sigma weight residual 139.87 125.08 14.79 1.00e+00 1.00e+00 2.19e+02 angle pdb=" PB ATP F1101 " pdb=" O3B ATP F1101 " pdb=" PG ATP F1101 " ideal model delta sigma weight residual 139.87 125.09 14.78 1.00e+00 1.00e+00 2.19e+02 angle pdb=" PB ATP A1101 " pdb=" O3B ATP A1101 " pdb=" PG ATP A1101 " ideal model delta sigma weight residual 139.87 125.09 14.78 1.00e+00 1.00e+00 2.18e+02 angle pdb=" PB ATP C1101 " pdb=" O3B ATP C1101 " pdb=" PG ATP C1101 " ideal model delta sigma weight residual 139.87 125.10 14.77 1.00e+00 1.00e+00 2.18e+02 ... (remaining 93055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 21599 17.32 - 34.64: 1549 34.64 - 51.96: 720 51.96 - 69.28: 206 69.28 - 86.60: 88 Dihedral angle restraints: 24162 sinusoidal: 13200 harmonic: 10962 Sorted by residual: dihedral pdb=" CA GLY C 324 " pdb=" C GLY C 324 " pdb=" N PRO C 325 " pdb=" CA PRO C 325 " ideal model delta harmonic sigma weight residual 0.00 27.26 -27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA GLY E 324 " pdb=" C GLY E 324 " pdb=" N PRO E 325 " pdb=" CA PRO E 325 " ideal model delta harmonic sigma weight residual 0.00 27.21 -27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLY A 324 " pdb=" C GLY A 324 " pdb=" N PRO A 325 " pdb=" CA PRO A 325 " ideal model delta harmonic sigma weight residual 0.00 27.20 -27.20 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 24159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 3605 0.125 - 0.251: 298 0.251 - 0.376: 74 0.376 - 0.501: 19 0.501 - 0.627: 6 Chirality restraints: 4002 Sorted by residual: chirality pdb=" CA LYS D 62 " pdb=" N LYS D 62 " pdb=" C LYS D 62 " pdb=" CB LYS D 62 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.81e+00 chirality pdb=" CA LYS E 62 " pdb=" N LYS E 62 " pdb=" C LYS E 62 " pdb=" CB LYS E 62 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.81e+00 chirality pdb=" CA LYS F 62 " pdb=" N LYS F 62 " pdb=" C LYS F 62 " pdb=" CB LYS F 62 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.78e+00 ... (remaining 3999 not shown) Planarity restraints: 7518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 464 " -0.227 2.00e-02 2.50e+03 4.66e-01 3.25e+03 pdb=" CG ASN F 464 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN F 464 " 0.224 2.00e-02 2.50e+03 pdb=" ND2 ASN F 464 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN F 464 " -0.782 2.00e-02 2.50e+03 pdb="HD22 ASN F 464 " 0.767 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 464 " 0.227 2.00e-02 2.50e+03 4.66e-01 3.25e+03 pdb=" CG ASN B 464 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 464 " -0.225 2.00e-02 2.50e+03 pdb=" ND2 ASN B 464 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 464 " 0.782 2.00e-02 2.50e+03 pdb="HD22 ASN B 464 " -0.766 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 464 " 0.227 2.00e-02 2.50e+03 4.66e-01 3.25e+03 pdb=" CG ASN A 464 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 464 " -0.225 2.00e-02 2.50e+03 pdb=" ND2 ASN A 464 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 464 " 0.782 2.00e-02 2.50e+03 pdb="HD22 ASN A 464 " -0.766 2.00e-02 2.50e+03 ... (remaining 7515 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 840 2.07 - 2.70: 84404 2.70 - 3.33: 144935 3.33 - 3.97: 197973 3.97 - 4.60: 307360 Nonbonded interactions: 735512 Sorted by model distance: nonbonded pdb=" HD2 HIS C 108 " pdb=" HH TYR C 174 " model vdw 1.437 2.100 nonbonded pdb=" HD2 HIS E 108 " pdb=" HH TYR E 174 " model vdw 1.437 2.100 nonbonded pdb=" HD2 HIS B 108 " pdb=" HH TYR B 174 " model vdw 1.437 2.100 nonbonded pdb=" HD2 HIS A 108 " pdb=" HH TYR A 174 " model vdw 1.437 2.100 nonbonded pdb=" HD2 HIS D 108 " pdb=" HH TYR D 174 " model vdw 1.437 2.100 ... (remaining 735507 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.720 Extract box with map and model: 1.800 Check model and map are aligned: 0.350 Set scattering table: 0.360 Process input model: 91.010 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.015 0.129 26088 Z= 0.995 Angle : 1.456 14.809 35430 Z= 0.957 Chirality : 0.090 0.627 4002 Planarity : 0.008 0.065 4482 Dihedral : 16.837 86.598 9762 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.06 % Favored : 93.75 % Rotamer: Outliers : 0.43 % Allowed : 11.32 % Favored : 88.25 % Cbeta Deviations : 0.97 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3168 helix: -0.25 (0.15), residues: 1092 sheet: -0.81 (0.21), residues: 540 loop : -1.60 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP F 466 HIS 0.010 0.002 HIS C 45 PHE 0.027 0.004 PHE F 315 TYR 0.028 0.004 TYR C 148 ARG 0.005 0.001 ARG E 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 222 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.9421 (mtt) cc_final: 0.9130 (mtt) REVERT: D 175 THR cc_start: 0.8964 (t) cc_final: 0.8711 (t) REVERT: D 425 ASP cc_start: 0.7792 (t0) cc_final: 0.7553 (t70) REVERT: E 175 THR cc_start: 0.8971 (t) cc_final: 0.8733 (t) REVERT: B 235 MET cc_start: 0.9397 (mtt) cc_final: 0.9113 (mtt) outliers start: 12 outliers final: 8 residues processed: 234 average time/residue: 2.3710 time to fit residues: 648.9998 Evaluate side-chains 188 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain B residue 499 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.7980 chunk 241 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 185 optimal weight: 0.5980 chunk 288 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26088 Z= 0.184 Angle : 0.603 7.532 35430 Z= 0.318 Chirality : 0.045 0.159 4002 Planarity : 0.004 0.053 4482 Dihedral : 9.164 57.035 3646 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 0.80 % Allowed : 12.73 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3168 helix: 0.78 (0.16), residues: 1056 sheet: -0.83 (0.21), residues: 564 loop : -1.36 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 437 HIS 0.004 0.001 HIS A 228 PHE 0.008 0.001 PHE E 225 TYR 0.009 0.001 TYR E 104 ARG 0.009 0.000 ARG D 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 4.039 Fit side-chains revert: symmetry clash REVERT: D 175 THR cc_start: 0.8903 (t) cc_final: 0.8618 (t) REVERT: E 28 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: E 175 THR cc_start: 0.8899 (t) cc_final: 0.8643 (t) REVERT: F 235 MET cc_start: 0.9356 (mtt) cc_final: 0.8880 (mtt) outliers start: 22 outliers final: 5 residues processed: 211 average time/residue: 3.1513 time to fit residues: 770.6583 Evaluate side-chains 183 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 177 time to evaluate : 3.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 488 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 312 optimal weight: 20.0000 chunk 257 optimal weight: 2.9990 chunk 286 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26088 Z= 0.290 Angle : 0.605 8.245 35430 Z= 0.321 Chirality : 0.046 0.158 4002 Planarity : 0.004 0.045 4482 Dihedral : 9.084 58.472 3634 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.51 % Favored : 95.30 % Rotamer: Outliers : 0.98 % Allowed : 11.28 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3168 helix: 0.92 (0.16), residues: 1062 sheet: -0.90 (0.21), residues: 564 loop : -1.17 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 402 HIS 0.005 0.001 HIS D 267 PHE 0.011 0.002 PHE C 173 TYR 0.014 0.002 TYR D 80 ARG 0.007 0.001 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 3.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7539 (mt0) REVERT: D 175 THR cc_start: 0.8887 (t) cc_final: 0.8634 (t) REVERT: E 175 THR cc_start: 0.8857 (t) cc_final: 0.8627 (t) REVERT: F 235 MET cc_start: 0.9315 (mtt) cc_final: 0.8885 (mtt) REVERT: F 331 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7205 (mt0) REVERT: C 197 MET cc_start: 0.8931 (mmp) cc_final: 0.8711 (mmm) REVERT: C 235 MET cc_start: 0.9322 (mtt) cc_final: 0.8883 (mtt) REVERT: B 331 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7456 (mt0) outliers start: 27 outliers final: 8 residues processed: 195 average time/residue: 2.8915 time to fit residues: 661.9495 Evaluate side-chains 182 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 331 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 307 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 275 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 HIS D 108 HIS E 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26088 Z= 0.266 Angle : 0.584 8.245 35430 Z= 0.308 Chirality : 0.045 0.154 4002 Planarity : 0.004 0.061 4482 Dihedral : 8.657 61.390 3634 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.95 % Favored : 95.86 % Rotamer: Outliers : 1.12 % Allowed : 11.57 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3168 helix: 1.09 (0.16), residues: 1056 sheet: -0.92 (0.21), residues: 564 loop : -1.04 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 402 HIS 0.005 0.001 HIS A 228 PHE 0.010 0.002 PHE A 187 TYR 0.012 0.002 TYR B 245 ARG 0.013 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 4.098 Fit side-chains revert: symmetry clash REVERT: A 331 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: D 175 THR cc_start: 0.8811 (t) cc_final: 0.8582 (t) REVERT: E 28 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: E 175 THR cc_start: 0.8797 (t) cc_final: 0.8595 (t) REVERT: F 197 MET cc_start: 0.9064 (mmp) cc_final: 0.8815 (mmm) REVERT: F 235 MET cc_start: 0.9300 (mtt) cc_final: 0.8868 (mtt) REVERT: F 331 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7124 (mt0) REVERT: C 425 ASP cc_start: 0.7923 (t0) cc_final: 0.7721 (t70) REVERT: B 331 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7508 (mt0) REVERT: B 375 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7356 (pm20) outliers start: 31 outliers final: 10 residues processed: 195 average time/residue: 3.0386 time to fit residues: 690.6509 Evaluate side-chains 182 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 375 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 262 optimal weight: 20.0000 chunk 212 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS F 108 HIS C 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 26088 Z= 0.302 Angle : 0.594 8.627 35430 Z= 0.315 Chirality : 0.046 0.154 4002 Planarity : 0.004 0.039 4482 Dihedral : 8.689 62.649 3634 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 1.05 % Allowed : 11.97 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3168 helix: 1.08 (0.16), residues: 1062 sheet: -0.97 (0.21), residues: 564 loop : -0.96 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 402 HIS 0.005 0.001 HIS A 228 PHE 0.011 0.002 PHE D 187 TYR 0.012 0.002 TYR A 245 ARG 0.004 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue LYS 497 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 5.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7562 (mt0) REVERT: D 175 THR cc_start: 0.8798 (t) cc_final: 0.8591 (t) REVERT: E 259 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: F 197 MET cc_start: 0.9075 (mmp) cc_final: 0.8839 (mmm) REVERT: F 235 MET cc_start: 0.9305 (mtt) cc_final: 0.8874 (mtt) REVERT: F 331 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7147 (mt0) REVERT: B 331 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7548 (mt0) outliers start: 29 outliers final: 14 residues processed: 192 average time/residue: 3.0649 time to fit residues: 687.2087 Evaluate side-chains 188 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 3.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 331 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 180 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 307 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: