Starting phenix.real_space_refine on Thu Sep 18 17:04:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e26_47439/09_2025/9e26_47439.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e26_47439/09_2025/9e26_47439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e26_47439/09_2025/9e26_47439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e26_47439/09_2025/9e26_47439.map" model { file = "/net/cci-nas-00/data/ceres_data/9e26_47439/09_2025/9e26_47439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e26_47439/09_2025/9e26_47439.cif" } resolution = 2.8 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 ------------------------------------------------------------------------------- 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= 0.044 sd= 0.115 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 10 5.49 5 Mg 4 5.21 5 S 102 5.16 5 C 11374 2.51 5 N 3422 2.21 5 O 3532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18444 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "E" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "F" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.20, per 1000 atoms: 0.28 Number of scatterers: 18444 At special positions: 0 Unit cell: (129.78, 145.23, 94.76, 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 102 16.00 P 10 15.00 Mg 4 11.99 O 3532 8.00 N 3422 7.00 C 11374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 871.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4644 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 12 sheets defined 45.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 80 through 97 Processing helix chain 'A' and resid 98 through 105 removed outlier: 3.593A pdb=" N LEU A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 126 Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'A' and resid 150 through 157 removed outlier: 4.246A pdb=" N LEU A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 361 through 372 removed outlier: 3.771A pdb=" N ASP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.554A pdb=" N ALA A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 106 through 126 Processing helix chain 'B' and resid 130 through 146 Processing helix chain 'B' and resid 150 through 157 removed outlier: 4.493A pdb=" N LEU B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 203 removed outlier: 4.015A pdb=" N VAL B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 337 through 346 Processing helix chain 'B' and resid 361 through 372 removed outlier: 3.979A pdb=" N ASP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 399 Processing helix chain 'B' and resid 405 through 417 Processing helix chain 'B' and resid 480 through 487 Processing helix chain 'B' and resid 489 through 501 Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 98 through 104 removed outlier: 3.581A pdb=" N LEU C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 126 Processing helix chain 'C' and resid 130 through 146 Processing helix chain 'C' and resid 150 through 157 removed outlier: 4.315A pdb=" N LEU C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 202 Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.592A pdb=" N LEU C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 337 through 346 Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.617A pdb=" N ASP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 400 Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 480 through 488 Processing helix chain 'C' and resid 489 through 501 Processing helix chain 'D' and resid 81 through 97 Processing helix chain 'D' and resid 98 through 105 removed outlier: 3.625A pdb=" N LEU D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 126 Processing helix chain 'D' and resid 130 through 146 Processing helix chain 'D' and resid 150 through 157 removed outlier: 4.249A pdb=" N LEU D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 337 through 346 Processing helix chain 'D' and resid 361 through 371 removed outlier: 3.799A pdb=" N ASP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'D' and resid 489 through 500 removed outlier: 3.522A pdb=" N ALA D 500 " --> pdb=" O ALA D 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 97 Processing helix chain 'E' and resid 98 through 105 removed outlier: 3.611A pdb=" N LEU E 105 " --> pdb=" O GLN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 125 Processing helix chain 'E' and resid 130 through 147 Processing helix chain 'E' and resid 150 through 157 removed outlier: 4.162A pdb=" N LEU E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 249 through 256 Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 286 through 295 Processing helix chain 'E' and resid 296 through 298 No H-bonds generated for 'chain 'E' and resid 296 through 298' Processing helix chain 'E' and resid 337 through 346 Processing helix chain 'E' and resid 361 through 372 removed outlier: 3.968A pdb=" N ASP E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 399 Processing helix chain 'E' and resid 405 through 417 Processing helix chain 'E' and resid 480 through 487 Processing helix chain 'E' and resid 489 through 501 Processing helix chain 'F' and resid 81 through 97 Processing helix chain 'F' and resid 98 through 105 Processing helix chain 'F' and resid 106 through 126 removed outlier: 3.859A pdb=" N GLY F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F 116 " --> pdb=" O GLU F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 146 Processing helix chain 'F' and resid 150 through 157 removed outlier: 4.351A pdb=" N LEU F 154 " --> pdb=" O PRO F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 244 through 248 removed outlier: 3.893A pdb=" N LYS F 247 " --> pdb=" O LYS F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 256 removed outlier: 4.112A pdb=" N LEU F 253 " --> pdb=" O THR F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 337 through 346 Processing helix chain 'F' and resid 361 through 373 removed outlier: 3.615A pdb=" N ASP F 365 " --> pdb=" O PRO F 361 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY F 373 " --> pdb=" O ALA F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 405 through 417 Processing helix chain 'F' and resid 480 through 488 Processing helix chain 'F' and resid 489 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 3.879A pdb=" N ASP A 162 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 320 through 324 removed outlier: 6.743A pdb=" N VAL A 304 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU A 323 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THR A 306 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 305 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLY A 356 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N CYS A 307 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL A 358 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A 378 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLY A 356 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR A 380 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS A 382 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A 278 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA A 423 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER A 280 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ARG A 425 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 420 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 436 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 11.250A pdb=" N ARG A 432 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N GLU A 456 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR A 434 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 454 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 436 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 448 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU A 442 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 467 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 182 removed outlier: 4.649A pdb=" N VAL B 171 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 162 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 320 through 324 removed outlier: 6.371A pdb=" N VAL B 305 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 380 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 379 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 278 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA B 423 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER B 280 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ARG B 425 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 420 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE B 436 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 11.157A pdb=" N ARG B 432 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLU B 456 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR B 434 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL B 454 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 436 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 448 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU B 442 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 467 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 178 through 182 removed outlier: 4.618A pdb=" N VAL C 171 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP C 162 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 320 through 324 removed outlier: 6.618A pdb=" N VAL C 305 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 380 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 278 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ALA C 423 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER C 280 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ARG C 425 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA C 424 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE C 433 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 11.560A pdb=" N ARG C 432 " --> pdb=" O GLU C 456 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N GLU C 456 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR C 434 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL C 454 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE C 436 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 448 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU C 442 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR C 455 " --> pdb=" O ARG C 471 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG C 471 " --> pdb=" O TYR C 455 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE C 457 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS C 469 " --> pdb=" O ILE C 457 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 178 through 182 removed outlier: 4.641A pdb=" N VAL D 171 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE D 172 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE D 163 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU D 174 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 320 through 324 removed outlier: 6.733A pdb=" N VAL D 304 " --> pdb=" O VAL D 321 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU D 323 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR D 306 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL D 305 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR D 380 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS D 435 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA D 424 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE D 433 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 11.269A pdb=" N ARG D 432 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 10.465A pdb=" N GLU D 456 " --> pdb=" O ARG D 432 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR D 434 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL D 454 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE D 436 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL D 448 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU D 442 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL D 467 " --> pdb=" O THR D 458 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 178 through 182 removed outlier: 4.589A pdb=" N VAL E 171 " --> pdb=" O THR E 182 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG E 170 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL E 165 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE E 172 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE E 163 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU E 174 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 320 through 324 removed outlier: 6.376A pdb=" N VAL E 305 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 380 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU E 277 " --> pdb=" O GLY E 379 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU E 381 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE E 279 " --> pdb=" O LEU E 381 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL E 278 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA E 423 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER E 280 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ARG E 425 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE E 420 " --> pdb=" O ILE E 436 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE E 436 " --> pdb=" O ILE E 420 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN E 422 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 17.116A pdb=" N ARG E 431 " --> pdb=" O THR E 458 " (cutoff:3.500A) removed outlier: 13.589A pdb=" N THR E 458 " --> pdb=" O ARG E 431 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N ILE E 433 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLU E 456 " --> pdb=" O ILE E 433 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS E 435 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL E 454 " --> pdb=" O HIS E 435 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR E 437 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU E 452 " --> pdb=" O THR E 437 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL E 439 " --> pdb=" O GLN E 450 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN E 450 " --> pdb=" O VAL E 439 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL E 467 " --> pdb=" O THR E 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 178 through 182 removed outlier: 4.627A pdb=" N VAL F 171 " --> pdb=" O THR F 182 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG F 170 " --> pdb=" O ASN F 166 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP F 162 " --> pdb=" O GLU F 174 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 320 through 324 removed outlier: 6.659A pdb=" N VAL F 305 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLY F 356 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N CYS F 307 " --> pdb=" O GLY F 356 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR F 380 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU F 357 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N HIS F 382 " --> pdb=" O GLU F 357 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL F 278 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA F 423 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER F 280 " --> pdb=" O ALA F 423 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ARG F 425 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA F 424 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE F 433 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N ARG F 432 " --> pdb=" O GLU F 456 " (cutoff:3.500A) removed outlier: 10.489A pdb=" N GLU F 456 " --> pdb=" O ARG F 432 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR F 434 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL F 454 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE F 436 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL F 448 " --> pdb=" O VAL F 440 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU F 442 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL F 446 " --> pdb=" O LEU F 442 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TYR F 455 " --> pdb=" O ARG F 471 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG F 471 " --> pdb=" O TYR F 455 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE F 457 " --> pdb=" O LYS F 469 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS F 469 " --> pdb=" O ILE F 457 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2937 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: 3.76 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6552 1.34 - 1.46: 3189 1.46 - 1.58: 8757 1.58 - 1.70: 10 1.70 - 1.81: 168 Bond restraints: 18676 Sorted by residual: bond pdb=" C VAL E 145 " pdb=" N LEU E 146 " ideal model delta sigma weight residual 1.332 1.357 -0.024 1.40e-02 5.10e+03 3.00e+00 bond pdb=" C VAL F 145 " pdb=" N LEU F 146 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.42e-02 4.96e+03 2.96e+00 bond pdb=" N LEU F 146 " pdb=" CA LEU F 146 " ideal model delta sigma weight residual 1.455 1.473 -0.018 1.29e-02 6.01e+03 2.05e+00 bond pdb=" C4 ADP E 602 " pdb=" C5 ADP E 602 " ideal model delta sigma weight residual 1.490 1.461 0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 1.97e+00 ... (remaining 18671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 24995 1.68 - 3.36: 259 3.36 - 5.04: 92 5.04 - 6.71: 19 6.71 - 8.39: 5 Bond angle restraints: 25370 Sorted by residual: angle pdb=" CG ARG F 491 " pdb=" CD ARG F 491 " pdb=" NE ARG F 491 " ideal model delta sigma weight residual 112.00 118.94 -6.94 2.20e+00 2.07e-01 9.94e+00 angle pdb=" CB MET A 399 " pdb=" CG MET A 399 " pdb=" SD MET A 399 " ideal model delta sigma weight residual 112.70 121.09 -8.39 3.00e+00 1.11e-01 7.83e+00 angle pdb=" C3' ATP A 602 " pdb=" C4' ATP A 602 " pdb=" C5' ATP A 602 " ideal model delta sigma weight residual 115.19 110.40 4.79 1.76e+00 3.23e-01 7.41e+00 angle pdb=" C2' ATP A 602 " pdb=" C3' ATP A 602 " pdb=" O3' ATP A 602 " ideal model delta sigma weight residual 111.83 104.97 6.86 2.67e+00 1.40e-01 6.61e+00 angle pdb=" CB ARG C 491 " pdb=" CG ARG C 491 " pdb=" CD ARG C 491 " ideal model delta sigma weight residual 111.30 117.06 -5.76 2.30e+00 1.89e-01 6.27e+00 ... (remaining 25365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 10387 17.46 - 34.92: 813 34.92 - 52.39: 207 52.39 - 69.85: 54 69.85 - 87.31: 23 Dihedral angle restraints: 11484 sinusoidal: 4284 harmonic: 7200 Sorted by residual: dihedral pdb=" CA HIS D 435 " pdb=" C HIS D 435 " pdb=" N ILE D 436 " pdb=" CA ILE D 436 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA HIS A 435 " pdb=" C HIS A 435 " pdb=" N ILE A 436 " pdb=" CA ILE A 436 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA HIS F 435 " pdb=" C HIS F 435 " pdb=" N ILE F 436 " pdb=" CA ILE F 436 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 11481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2523 0.060 - 0.120: 452 0.120 - 0.179: 29 0.179 - 0.239: 0 0.239 - 0.299: 6 Chirality restraints: 3010 Sorted by residual: chirality pdb=" C3' ATP A 602 " pdb=" C2' ATP A 602 " pdb=" C4' ATP A 602 " pdb=" O3' ATP A 602 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C2' ATP D 602 " pdb=" C1' ATP D 602 " pdb=" C3' ATP D 602 " pdb=" O2' ATP D 602 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' ATP A 602 " pdb=" C1' ATP A 602 " pdb=" C3' ATP A 602 " pdb=" O2' ATP A 602 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 3007 not shown) Planarity restraints: 3364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 145 " -0.024 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C VAL E 145 " 0.081 2.00e-02 2.50e+03 pdb=" O VAL E 145 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU E 146 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 145 " 0.024 2.00e-02 2.50e+03 4.64e-02 2.15e+01 pdb=" C VAL F 145 " -0.080 2.00e-02 2.50e+03 pdb=" O VAL F 145 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU F 146 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 491 " -0.255 9.50e-02 1.11e+02 1.15e-01 9.01e+00 pdb=" NE ARG C 491 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 491 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C 491 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 491 " -0.003 2.00e-02 2.50e+03 ... (remaining 3361 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 146 2.49 - 3.09: 14455 3.09 - 3.69: 28311 3.69 - 4.30: 41231 4.30 - 4.90: 70423 Nonbonded interactions: 154566 Sorted by model distance: nonbonded pdb=" OG1 THR A 288 " pdb="MG MG A 601 " model vdw 1.886 2.170 nonbonded pdb=" OG1 THR D 288 " pdb="MG MG D 601 " model vdw 1.915 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2B ATP D 602 " model vdw 1.924 2.170 nonbonded pdb=" OG1 THR E 288 " pdb="MG MG E 601 " model vdw 1.929 2.170 nonbonded pdb=" OG1 THR B 288 " pdb="MG MG B 602 " model vdw 1.945 2.170 ... (remaining 154561 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 80 through 501) selection = (chain 'B' and resid 80 through 501) selection = chain 'C' selection = (chain 'D' and resid 80 through 501) selection = (chain 'E' and resid 80 through 501) 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: 0.040 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.040 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 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 : 0.005 0.040 18676 Z= 0.210 Angle : 0.535 8.393 25370 Z= 0.269 Chirality : 0.046 0.299 3010 Planarity : 0.004 0.115 3364 Dihedral : 14.678 87.311 6840 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.07 % Allowed : 10.14 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.74 (0.18), residues: 2520 helix: 2.62 (0.16), residues: 1140 sheet: -0.61 (0.23), residues: 472 loop : 0.35 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 491 TYR 0.006 0.001 TYR D 487 PHE 0.005 0.001 PHE D 480 TRP 0.004 0.001 TRP A 481 HIS 0.003 0.001 HIS E 382 Details of bonding type rmsd covalent geometry : bond 0.00470 (18676) covalent geometry : angle 0.53466 (25370) hydrogen bonds : bond 0.11418 ( 1004) hydrogen bonds : angle 5.63490 ( 2937) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 748 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ILE cc_start: 0.7801 (mt) cc_final: 0.7153 (mt) REVERT: A 324 GLU cc_start: 0.6499 (tt0) cc_final: 0.6273 (tp30) REVERT: A 414 VAL cc_start: 0.7811 (t) cc_final: 0.7299 (p) REVERT: A 465 LYS cc_start: 0.5440 (mmmm) cc_final: 0.5063 (mtpp) REVERT: B 225 ASN cc_start: 0.7239 (t0) cc_final: 0.7014 (t0) REVERT: B 250 MET cc_start: 0.7076 (tpp) cc_final: 0.6669 (tpt) REVERT: B 465 LYS cc_start: 0.6633 (mmtp) cc_final: 0.6347 (tmtt) REVERT: C 171 VAL cc_start: 0.7248 (t) cc_final: 0.7015 (t) REVERT: C 298 ILE cc_start: 0.6915 (mt) cc_final: 0.6679 (mt) REVERT: C 299 ASP cc_start: 0.7424 (t0) cc_final: 0.7125 (t70) REVERT: C 325 THR cc_start: 0.6104 (p) cc_final: 0.5729 (p) REVERT: D 247 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7940 (tttt) REVERT: D 279 ILE cc_start: 0.7829 (mm) cc_final: 0.7529 (mm) REVERT: D 324 GLU cc_start: 0.8283 (tt0) cc_final: 0.8045 (tm-30) REVERT: D 351 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7035 (mp0) REVERT: E 173 ILE cc_start: 0.8067 (pt) cc_final: 0.7549 (pp) REVERT: E 178 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7542 (mmmt) REVERT: E 191 GLN cc_start: 0.9157 (tt0) cc_final: 0.8891 (tt0) REVERT: E 193 MET cc_start: 0.8552 (tpt) cc_final: 0.8221 (tpp) REVERT: E 277 LEU cc_start: 0.8110 (tp) cc_final: 0.7554 (mt) REVERT: E 324 GLU cc_start: 0.7317 (tp30) cc_final: 0.7090 (tp30) REVERT: E 345 CYS cc_start: 0.8456 (m) cc_final: 0.7851 (m) REVERT: E 395 SER cc_start: 0.7007 (m) cc_final: 0.6684 (p) REVERT: E 443 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6206 (mp0) REVERT: E 453 PHE cc_start: 0.6852 (t80) cc_final: 0.6560 (m-80) REVERT: F 244 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7246 (mptp) REVERT: F 289 THR cc_start: 0.8131 (m) cc_final: 0.7914 (p) REVERT: F 409 ILE cc_start: 0.5523 (mt) cc_final: 0.5316 (mt) outliers start: 19 outliers final: 6 residues processed: 761 average time/residue: 0.6225 time to fit residues: 530.9288 Evaluate side-chains 467 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 460 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 244 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN B 180 GLN C 180 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN D 344 ASN E 166 ASN E 202 GLN E 225 ASN E 344 ASN E 450 GLN F 435 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.108353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.087182 restraints weight = 41868.612| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.24 r_work: 0.3041 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 18676 Z= 0.297 Angle : 0.944 14.057 25370 Z= 0.480 Chirality : 0.056 0.238 3010 Planarity : 0.008 0.179 3364 Dihedral : 7.344 75.503 2859 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 8.95 % Allowed : 20.50 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.17), residues: 2520 helix: 1.40 (0.15), residues: 1164 sheet: -0.70 (0.21), residues: 574 loop : 0.40 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 347 TYR 0.025 0.003 TYR B 148 PHE 0.026 0.003 PHE A 297 TRP 0.046 0.003 TRP F 481 HIS 0.007 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00668 (18676) covalent geometry : angle 0.94418 (25370) hydrogen bonds : bond 0.04140 ( 1004) hydrogen bonds : angle 4.67289 ( 2937) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 521 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8994 (mm) REVERT: A 202 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8344 (tm-30) REVERT: A 215 ASP cc_start: 0.8596 (t0) cc_final: 0.8112 (t0) REVERT: A 218 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8761 (mp) REVERT: A 244 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7140 (pttm) REVERT: A 246 ASP cc_start: 0.8758 (t0) cc_final: 0.8305 (p0) REVERT: A 247 LYS cc_start: 0.8152 (pmmt) cc_final: 0.7156 (mptp) REVERT: A 250 MET cc_start: 0.6285 (pmm) cc_final: 0.5570 (tpp) REVERT: A 265 ARG cc_start: 0.7808 (mmp80) cc_final: 0.7318 (mtp-110) REVERT: A 283 THR cc_start: 0.8539 (t) cc_final: 0.8114 (t) REVERT: A 298 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8893 (mt) REVERT: A 314 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 324 GLU cc_start: 0.8235 (tt0) cc_final: 0.7204 (tp30) REVERT: A 371 ASN cc_start: 0.8380 (t0) cc_final: 0.8158 (t0) REVERT: A 392 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7921 (ttm-80) REVERT: A 451 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7932 (t0) REVERT: A 469 LYS cc_start: 0.8205 (tptp) cc_final: 0.7684 (tptt) REVERT: A 482 ASP cc_start: 0.8911 (t0) cc_final: 0.8310 (p0) REVERT: B 162 ASP cc_start: 0.7063 (m-30) cc_final: 0.6562 (m-30) REVERT: B 174 GLU cc_start: 0.7816 (tt0) cc_final: 0.7584 (tt0) REVERT: B 180 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7973 (pp30) REVERT: B 186 PHE cc_start: 0.8614 (m-80) cc_final: 0.8146 (m-10) REVERT: B 276 ASN cc_start: 0.8096 (m-40) cc_final: 0.7771 (m-40) REVERT: B 323 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8026 (mt) REVERT: B 324 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6735 (mm-30) REVERT: B 339 ARG cc_start: 0.8446 (ttp-170) cc_final: 0.7907 (ttm-80) REVERT: B 340 ASP cc_start: 0.7965 (m-30) cc_final: 0.7761 (m-30) REVERT: B 367 LEU cc_start: 0.8487 (mp) cc_final: 0.8265 (mt) REVERT: B 393 ILE cc_start: 0.8276 (mm) cc_final: 0.8035 (mt) REVERT: B 452 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8893 (tt) REVERT: B 456 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: B 473 THR cc_start: 0.8534 (m) cc_final: 0.8236 (p) REVERT: C 163 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7400 (mt) REVERT: C 164 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8592 (mpp) REVERT: C 174 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7134 (tp30) REVERT: C 178 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7947 (tmmt) REVERT: C 273 CYS cc_start: 0.8654 (m) cc_final: 0.7889 (p) REVERT: C 324 GLU cc_start: 0.8429 (tt0) cc_final: 0.8175 (tt0) REVERT: C 378 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8177 (mtp) REVERT: C 498 ASP cc_start: 0.8945 (p0) cc_final: 0.8702 (p0) REVERT: D 308 GLU cc_start: 0.7949 (tt0) cc_final: 0.7744 (pt0) REVERT: D 314 GLN cc_start: 0.8533 (mp10) cc_final: 0.8325 (mp10) REVERT: D 351 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8111 (mp0) REVERT: D 390 ILE cc_start: 0.8686 (pp) cc_final: 0.8425 (pt) REVERT: D 393 ILE cc_start: 0.8936 (mt) cc_final: 0.8691 (mp) REVERT: D 469 LYS cc_start: 0.8925 (ptmm) cc_final: 0.8372 (ptmm) REVERT: E 164 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8217 (mtt) REVERT: E 180 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: E 191 GLN cc_start: 0.9287 (tt0) cc_final: 0.8791 (tt0) REVERT: E 193 MET cc_start: 0.8752 (tpt) cc_final: 0.8372 (tpp) REVERT: E 306 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8736 (m) REVERT: E 324 GLU cc_start: 0.8616 (tp30) cc_final: 0.7943 (mm-30) REVERT: E 338 MET cc_start: 0.8608 (tpp) cc_final: 0.8205 (tpp) REVERT: E 344 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8052 (t0) REVERT: E 396 MET cc_start: 0.8883 (mtt) cc_final: 0.8657 (mtp) REVERT: E 443 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7707 (mm-30) REVERT: E 481 TRP cc_start: 0.8182 (t-100) cc_final: 0.7977 (t-100) REVERT: E 492 GLU cc_start: 0.7925 (tp30) cc_final: 0.7018 (tp30) REVERT: E 495 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8080 (pt0) REVERT: E 498 ASP cc_start: 0.8255 (t0) cc_final: 0.7952 (p0) REVERT: F 160 ILE cc_start: 0.8680 (mt) cc_final: 0.8161 (mp) REVERT: F 180 GLN cc_start: 0.9264 (pt0) cc_final: 0.8577 (pm20) REVERT: F 197 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8754 (mt0) REVERT: F 206 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7806 (ptm-80) REVERT: F 242 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9058 (mtpt) REVERT: F 244 LYS cc_start: 0.8522 (tppt) cc_final: 0.8261 (tppt) REVERT: F 245 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7563 (mppt) REVERT: F 289 THR cc_start: 0.9126 (m) cc_final: 0.8748 (p) REVERT: F 341 LEU cc_start: 0.8424 (mt) cc_final: 0.8137 (tp) REVERT: F 345 CYS cc_start: 0.8910 (m) cc_final: 0.8608 (m) REVERT: F 407 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7915 (tptp) REVERT: F 411 GLU cc_start: 0.8705 (pp20) cc_final: 0.8413 (tm-30) REVERT: F 412 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8132 (ttt) REVERT: F 421 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7955 (mp) REVERT: F 431 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.7954 (ttm170) outliers start: 159 outliers final: 40 residues processed: 606 average time/residue: 0.6121 time to fit residues: 415.2406 Evaluate side-chains 453 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 389 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 486 TYR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 206 ARG Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 470 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 62 optimal weight: 0.6980 chunk 187 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 150 optimal weight: 0.0770 chunk 162 optimal weight: 0.2980 chunk 74 optimal weight: 9.9990 chunk 168 optimal weight: 120.0000 chunk 199 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 231 optimal weight: 0.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 374 HIS A 470 HIS ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 292 ASN C 384 ASN D 191 GLN D 225 ASN D 292 ASN E 225 ASN E 314 GLN E 344 ASN ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS F 422 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.104723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.082462 restraints weight = 40900.096| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.19 r_work: 0.3041 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18676 Z= 0.138 Angle : 0.695 11.321 25370 Z= 0.341 Chirality : 0.047 0.177 3010 Planarity : 0.005 0.051 3364 Dihedral : 6.549 75.236 2847 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 6.25 % Allowed : 26.35 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.17), residues: 2520 helix: 1.86 (0.15), residues: 1152 sheet: -0.55 (0.21), residues: 574 loop : 0.27 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 206 TYR 0.013 0.001 TYR D 486 PHE 0.020 0.002 PHE E 453 TRP 0.008 0.001 TRP F 481 HIS 0.003 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00320 (18676) covalent geometry : angle 0.69519 (25370) hydrogen bonds : bond 0.03219 ( 1004) hydrogen bonds : angle 4.20192 ( 2937) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 416 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8975 (pptt) cc_final: 0.8634 (pptt) REVERT: A 180 GLN cc_start: 0.8649 (pt0) cc_final: 0.8410 (pm20) REVERT: A 202 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8381 (tm-30) REVERT: A 215 ASP cc_start: 0.8446 (t0) cc_final: 0.8178 (t0) REVERT: A 246 ASP cc_start: 0.8734 (t0) cc_final: 0.8206 (p0) REVERT: A 247 LYS cc_start: 0.7988 (pmmt) cc_final: 0.7499 (pmmt) REVERT: A 250 MET cc_start: 0.6514 (pmm) cc_final: 0.6059 (tpp) REVERT: A 265 ARG cc_start: 0.7977 (mmp80) cc_final: 0.7770 (mtp180) REVERT: A 298 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8978 (mt) REVERT: A 314 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8073 (tm-30) REVERT: A 324 GLU cc_start: 0.8315 (tt0) cc_final: 0.7486 (tp30) REVERT: A 340 ASP cc_start: 0.8880 (t70) cc_final: 0.8372 (m-30) REVERT: A 365 ASP cc_start: 0.8770 (t0) cc_final: 0.8533 (m-30) REVERT: A 450 GLN cc_start: 0.8048 (pp30) cc_final: 0.7747 (pp30) REVERT: A 469 LYS cc_start: 0.7604 (tptp) cc_final: 0.7277 (ttpp) REVERT: A 482 ASP cc_start: 0.9018 (t0) cc_final: 0.8491 (p0) REVERT: B 174 GLU cc_start: 0.7961 (tt0) cc_final: 0.7688 (tt0) REVERT: B 180 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: B 250 MET cc_start: 0.8116 (tpp) cc_final: 0.7913 (tpp) REVERT: B 276 ASN cc_start: 0.8198 (m-40) cc_final: 0.7904 (m-40) REVERT: B 456 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7318 (pm20) REVERT: C 174 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: C 193 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8568 (mmt) REVERT: C 273 CYS cc_start: 0.8462 (m) cc_final: 0.7891 (p) REVERT: C 324 GLU cc_start: 0.8560 (tt0) cc_final: 0.8348 (tt0) REVERT: C 368 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8391 (mm-40) REVERT: C 378 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8341 (mtp) REVERT: C 450 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8519 (tm-30) REVERT: D 211 SER cc_start: 0.8958 (t) cc_final: 0.8753 (t) REVERT: D 308 GLU cc_start: 0.7739 (tt0) cc_final: 0.7485 (pt0) REVERT: D 314 GLN cc_start: 0.8515 (mp10) cc_final: 0.8201 (mp10) REVERT: D 351 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8112 (mp0) REVERT: D 469 LYS cc_start: 0.8903 (ptmm) cc_final: 0.8375 (ptmm) REVERT: E 174 GLU cc_start: 0.7349 (mp0) cc_final: 0.7084 (mp0) REVERT: E 191 GLN cc_start: 0.9263 (tt0) cc_final: 0.8772 (tt0) REVERT: E 193 MET cc_start: 0.8755 (tpt) cc_final: 0.8328 (tpp) REVERT: E 215 ASP cc_start: 0.8786 (p0) cc_final: 0.8461 (t0) REVERT: E 324 GLU cc_start: 0.8636 (tp30) cc_final: 0.8090 (mm-30) REVERT: E 338 MET cc_start: 0.8588 (tpp) cc_final: 0.8151 (tpp) REVERT: E 344 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8184 (t0) REVERT: E 396 MET cc_start: 0.8865 (mtt) cc_final: 0.8648 (mtp) REVERT: E 481 TRP cc_start: 0.8180 (t-100) cc_final: 0.7876 (t-100) REVERT: E 492 GLU cc_start: 0.7885 (tp30) cc_final: 0.6868 (tp30) REVERT: E 495 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8035 (pt0) REVERT: E 498 ASP cc_start: 0.8258 (t0) cc_final: 0.7814 (p0) REVERT: F 160 ILE cc_start: 0.8648 (mt) cc_final: 0.8198 (mp) REVERT: F 242 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8887 (mtpt) REVERT: F 245 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7701 (mppt) REVERT: F 247 LYS cc_start: 0.9022 (ptpp) cc_final: 0.8731 (mppt) REVERT: F 289 THR cc_start: 0.9152 (m) cc_final: 0.8866 (p) REVERT: F 312 GLU cc_start: 0.7672 (pm20) cc_final: 0.7360 (pm20) REVERT: F 345 CYS cc_start: 0.8807 (m) cc_final: 0.8412 (m) REVERT: F 388 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8442 (tm-30) REVERT: F 410 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8174 (mtpp) REVERT: F 412 MET cc_start: 0.8560 (mtp) cc_final: 0.8231 (ttt) REVERT: F 421 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8088 (mp) outliers start: 111 outliers final: 36 residues processed: 480 average time/residue: 0.6145 time to fit residues: 329.8976 Evaluate side-chains 408 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 361 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 454 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 20 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 232 optimal weight: 30.0000 chunk 115 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 173 optimal weight: 50.0000 chunk 90 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 180 GLN C 166 ASN C 292 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN F 252 ASN F 344 ASN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.091928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.069866 restraints weight = 41987.847| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.13 r_work: 0.2941 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.8138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 18676 Z= 0.199 Angle : 0.716 10.480 25370 Z= 0.354 Chirality : 0.048 0.196 3010 Planarity : 0.005 0.060 3364 Dihedral : 6.294 78.659 2847 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 6.87 % Allowed : 26.07 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.17), residues: 2520 helix: 1.82 (0.15), residues: 1156 sheet: -0.62 (0.21), residues: 566 loop : 0.19 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 491 TYR 0.012 0.002 TYR D 486 PHE 0.021 0.002 PHE D 243 TRP 0.010 0.002 TRP A 481 HIS 0.004 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00474 (18676) covalent geometry : angle 0.71580 (25370) hydrogen bonds : bond 0.03162 ( 1004) hydrogen bonds : angle 4.13424 ( 2937) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 387 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8202 (tm) REVERT: A 202 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 247 LYS cc_start: 0.8345 (pmmt) cc_final: 0.7817 (pmmt) REVERT: A 250 MET cc_start: 0.7183 (pmm) cc_final: 0.6963 (tpt) REVERT: A 324 GLU cc_start: 0.8732 (tt0) cc_final: 0.8062 (tt0) REVERT: A 340 ASP cc_start: 0.8949 (t70) cc_final: 0.8739 (m-30) REVERT: A 398 THR cc_start: 0.9280 (m) cc_final: 0.8817 (p) REVERT: A 411 GLU cc_start: 0.8584 (pp20) cc_final: 0.8301 (pp20) REVERT: A 450 GLN cc_start: 0.8383 (pp30) cc_final: 0.7793 (pp30) REVERT: A 482 ASP cc_start: 0.9183 (t0) cc_final: 0.8799 (p0) REVERT: B 162 ASP cc_start: 0.7698 (m-30) cc_final: 0.7154 (m-30) REVERT: B 174 GLU cc_start: 0.8225 (tt0) cc_final: 0.7829 (tt0) REVERT: B 186 PHE cc_start: 0.8827 (m-10) cc_final: 0.8503 (m-10) REVERT: B 195 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8161 (mt) REVERT: B 250 MET cc_start: 0.8451 (tpp) cc_final: 0.8233 (tpp) REVERT: B 338 MET cc_start: 0.9127 (mmt) cc_final: 0.8762 (mmt) REVERT: B 339 ARG cc_start: 0.8677 (ttp-170) cc_final: 0.8210 (ttm-80) REVERT: B 343 LYS cc_start: 0.9189 (mtmp) cc_final: 0.8891 (mttp) REVERT: B 456 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: B 498 ASP cc_start: 0.8007 (p0) cc_final: 0.7748 (m-30) REVERT: C 273 CYS cc_start: 0.8905 (m) cc_final: 0.8037 (p) REVERT: C 324 GLU cc_start: 0.8851 (tt0) cc_final: 0.8498 (tt0) REVERT: C 337 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8746 (p) REVERT: C 343 LYS cc_start: 0.9197 (mttp) cc_final: 0.8950 (mmtp) REVERT: C 370 MET cc_start: 0.9168 (mtt) cc_final: 0.8797 (mtt) REVERT: C 378 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8664 (mtt) REVERT: C 407 LYS cc_start: 0.8826 (tppp) cc_final: 0.8106 (tppt) REVERT: C 411 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8597 (mp0) REVERT: C 498 ASP cc_start: 0.9156 (OUTLIER) cc_final: 0.8858 (p0) REVERT: D 164 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8755 (ptp) REVERT: D 211 SER cc_start: 0.9037 (t) cc_final: 0.8827 (t) REVERT: D 351 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8313 (mp0) REVERT: D 394 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8698 (tt0) REVERT: D 453 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8629 (m-80) REVERT: D 469 LYS cc_start: 0.9193 (ptmm) cc_final: 0.8757 (ptmm) REVERT: E 186 PHE cc_start: 0.8352 (m-10) cc_final: 0.7856 (m-80) REVERT: E 191 GLN cc_start: 0.9266 (tt0) cc_final: 0.8677 (tt0) REVERT: E 193 MET cc_start: 0.8748 (tpt) cc_final: 0.8289 (tpp) REVERT: E 213 ILE cc_start: 0.9275 (pt) cc_final: 0.8978 (pp) REVERT: E 251 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8375 (mmmm) REVERT: E 324 GLU cc_start: 0.8738 (tp30) cc_final: 0.8109 (mm-30) REVERT: E 338 MET cc_start: 0.8860 (tpp) cc_final: 0.8541 (tpp) REVERT: E 443 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7964 (mm-30) REVERT: E 445 ASP cc_start: 0.8965 (t0) cc_final: 0.8463 (t0) REVERT: E 495 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8337 (pt0) REVERT: E 498 ASP cc_start: 0.8418 (t0) cc_final: 0.7977 (p0) REVERT: F 160 ILE cc_start: 0.8900 (mt) cc_final: 0.8681 (mt) REVERT: F 197 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8762 (mt0) REVERT: F 242 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8889 (mtpt) REVERT: F 294 MET cc_start: 0.9197 (tpp) cc_final: 0.8971 (tpp) REVERT: F 312 GLU cc_start: 0.7987 (pm20) cc_final: 0.7727 (pm20) REVERT: F 340 ASP cc_start: 0.8826 (m-30) cc_final: 0.8595 (m-30) REVERT: F 345 CYS cc_start: 0.8975 (m) cc_final: 0.8685 (m) REVERT: F 385 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8700 (p) REVERT: F 388 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: F 422 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7216 (tp40) outliers start: 122 outliers final: 39 residues processed: 466 average time/residue: 0.6566 time to fit residues: 340.7734 Evaluate side-chains 383 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 332 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 437 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 139 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 33 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS E 314 GLN ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.101918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.080079 restraints weight = 41443.895| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.20 r_work: 0.2894 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.9127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18676 Z= 0.195 Angle : 0.695 10.532 25370 Z= 0.344 Chirality : 0.048 0.175 3010 Planarity : 0.006 0.089 3364 Dihedral : 6.322 83.912 2847 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 6.48 % Allowed : 27.48 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.15 (0.17), residues: 2520 helix: 1.92 (0.16), residues: 1148 sheet: -0.31 (0.22), residues: 528 loop : -0.00 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 477 TYR 0.013 0.002 TYR D 402 PHE 0.022 0.002 PHE B 243 TRP 0.012 0.002 TRP A 481 HIS 0.003 0.001 HIS E 382 Details of bonding type rmsd covalent geometry : bond 0.00467 (18676) covalent geometry : angle 0.69452 (25370) hydrogen bonds : bond 0.03120 ( 1004) hydrogen bonds : angle 4.04885 ( 2937) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 356 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9065 (pptt) cc_final: 0.8754 (pptt) REVERT: A 180 GLN cc_start: 0.9202 (pt0) cc_final: 0.8700 (pt0) REVERT: A 192 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8289 (tm) REVERT: A 197 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8624 (mt0) REVERT: A 202 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8386 (tm-30) REVERT: A 242 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8568 (mtmt) REVERT: A 247 LYS cc_start: 0.8272 (pmmt) cc_final: 0.7777 (mptp) REVERT: A 251 LYS cc_start: 0.9298 (ptmm) cc_final: 0.9021 (ptmm) REVERT: A 324 GLU cc_start: 0.8821 (tt0) cc_final: 0.8092 (tt0) REVERT: A 347 ARG cc_start: 0.8724 (ttp-110) cc_final: 0.8390 (ttm110) REVERT: A 365 ASP cc_start: 0.8909 (m-30) cc_final: 0.8687 (m-30) REVERT: A 407 LYS cc_start: 0.9208 (tppp) cc_final: 0.8794 (tppt) REVERT: A 438 GLU cc_start: 0.7923 (mp0) cc_final: 0.7683 (mp0) REVERT: A 440 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8435 (m) REVERT: A 463 HIS cc_start: 0.8576 (m90) cc_final: 0.8299 (m90) REVERT: A 482 ASP cc_start: 0.9274 (t0) cc_final: 0.8936 (p0) REVERT: A 493 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7743 (mm) REVERT: B 162 ASP cc_start: 0.7812 (m-30) cc_final: 0.7290 (m-30) REVERT: B 174 GLU cc_start: 0.8385 (tt0) cc_final: 0.8002 (tt0) REVERT: B 180 GLN cc_start: 0.8933 (pp30) cc_final: 0.8695 (pp30) REVERT: B 324 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8398 (mt-10) REVERT: B 339 ARG cc_start: 0.8736 (ttp-170) cc_final: 0.8260 (ttm-80) REVERT: B 370 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7648 (mmt) REVERT: B 456 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: B 498 ASP cc_start: 0.8103 (p0) cc_final: 0.7870 (m-30) REVERT: C 174 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: C 178 LYS cc_start: 0.8515 (tmmt) cc_final: 0.8153 (tmmt) REVERT: C 238 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9052 (pp) REVERT: C 273 CYS cc_start: 0.8851 (m) cc_final: 0.7924 (p) REVERT: C 279 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7642 (mt) REVERT: C 324 GLU cc_start: 0.8843 (tt0) cc_final: 0.8497 (tt0) REVERT: C 337 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8997 (p) REVERT: C 339 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8806 (tpp80) REVERT: C 370 MET cc_start: 0.9246 (mtt) cc_final: 0.8973 (mtt) REVERT: C 407 LYS cc_start: 0.8939 (tppp) cc_final: 0.8202 (tppt) REVERT: C 411 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8661 (mp0) REVERT: C 427 ARG cc_start: 0.8473 (ttp80) cc_final: 0.8150 (tmm-80) REVERT: D 164 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8806 (ptp) REVERT: D 174 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8099 (mm-30) REVERT: D 211 SER cc_start: 0.9082 (t) cc_final: 0.8696 (p) REVERT: D 339 ARG cc_start: 0.8690 (ttm170) cc_final: 0.8470 (ttm-80) REVERT: D 351 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8417 (mp0) REVERT: D 392 ARG cc_start: 0.9122 (mmm-85) cc_final: 0.8806 (mmm-85) REVERT: D 469 LYS cc_start: 0.9207 (ptmm) cc_final: 0.8873 (ptmm) REVERT: D 479 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7809 (mtp85) REVERT: E 180 GLN cc_start: 0.9077 (pm20) cc_final: 0.8701 (pm20) REVERT: E 186 PHE cc_start: 0.8641 (m-10) cc_final: 0.8203 (m-80) REVERT: E 191 GLN cc_start: 0.9282 (tt0) cc_final: 0.8581 (tt0) REVERT: E 193 MET cc_start: 0.8594 (tpt) cc_final: 0.8237 (tpp) REVERT: E 213 ILE cc_start: 0.9239 (pt) cc_final: 0.8954 (pp) REVERT: E 244 LYS cc_start: 0.8803 (mtpm) cc_final: 0.7997 (tttp) REVERT: E 324 GLU cc_start: 0.8853 (tp30) cc_final: 0.8337 (mm-30) REVERT: E 348 MET cc_start: 0.9436 (mtp) cc_final: 0.9184 (mtt) REVERT: E 407 LYS cc_start: 0.8868 (tttp) cc_final: 0.8524 (tttp) REVERT: E 412 MET cc_start: 0.9086 (mtm) cc_final: 0.8647 (mtm) REVERT: E 445 ASP cc_start: 0.9039 (t0) cc_final: 0.8440 (t0) REVERT: E 495 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8650 (pt0) REVERT: E 498 ASP cc_start: 0.8552 (t0) cc_final: 0.8005 (t0) REVERT: F 160 ILE cc_start: 0.9012 (mt) cc_final: 0.8566 (mp) REVERT: F 206 ARG cc_start: 0.8423 (ptm-80) cc_final: 0.7945 (ptm-80) REVERT: F 242 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9136 (mtpt) REVERT: F 246 ASP cc_start: 0.8246 (m-30) cc_final: 0.7795 (m-30) REVERT: F 267 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8823 (mm) REVERT: F 294 MET cc_start: 0.9421 (tpp) cc_final: 0.8935 (tpt) REVERT: F 314 GLN cc_start: 0.8559 (mm110) cc_final: 0.8352 (mm110) REVERT: F 345 CYS cc_start: 0.9031 (m) cc_final: 0.8716 (m) REVERT: F 385 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8718 (p) outliers start: 115 outliers final: 35 residues processed: 436 average time/residue: 0.6757 time to fit residues: 325.6290 Evaluate side-chains 346 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 294 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 472 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 49 optimal weight: 40.0000 chunk 1 optimal weight: 0.7980 chunk 240 optimal weight: 10.0000 chunk 249 optimal weight: 0.2980 chunk 169 optimal weight: 40.0000 chunk 62 optimal weight: 30.0000 chunk 194 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 216 optimal weight: 30.0000 chunk 87 optimal weight: 40.0000 chunk 17 optimal weight: 0.9980 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 GLN B 450 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN D 450 GLN E 202 GLN E 314 GLN E 344 ASN E 450 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.089513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067609 restraints weight = 41865.398| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.09 r_work: 0.2882 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.9381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18676 Z= 0.161 Angle : 0.676 10.217 25370 Z= 0.332 Chirality : 0.047 0.172 3010 Planarity : 0.005 0.065 3364 Dihedral : 6.227 82.176 2845 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.57 % Allowed : 28.49 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.17), residues: 2520 helix: 2.04 (0.16), residues: 1146 sheet: -0.25 (0.22), residues: 502 loop : -0.09 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 206 TYR 0.009 0.001 TYR F 486 PHE 0.035 0.002 PHE D 243 TRP 0.009 0.001 TRP A 481 HIS 0.019 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00387 (18676) covalent geometry : angle 0.67622 (25370) hydrogen bonds : bond 0.02935 ( 1004) hydrogen bonds : angle 3.95957 ( 2937) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 335 time to evaluate : 0.636 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: A 192 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8291 (tm) REVERT: A 202 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8437 (tm-30) REVERT: A 242 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8656 (mtmt) REVERT: A 243 PHE cc_start: 0.8723 (t80) cc_final: 0.8381 (t80) REVERT: A 244 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.6521 (pttm) REVERT: A 246 ASP cc_start: 0.8490 (t0) cc_final: 0.8128 (p0) REVERT: A 324 GLU cc_start: 0.8780 (tt0) cc_final: 0.8084 (tt0) REVERT: A 365 ASP cc_start: 0.8698 (m-30) cc_final: 0.8492 (m-30) REVERT: A 407 LYS cc_start: 0.9293 (tppp) cc_final: 0.8551 (tppt) REVERT: A 438 GLU cc_start: 0.8043 (mp0) cc_final: 0.7811 (mp0) REVERT: A 440 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8501 (m) REVERT: A 463 HIS cc_start: 0.8642 (m90) cc_final: 0.8360 (m90) REVERT: A 482 ASP cc_start: 0.9289 (t0) cc_final: 0.9040 (p0) REVERT: B 162 ASP cc_start: 0.7881 (m-30) cc_final: 0.7511 (m-30) REVERT: B 174 GLU cc_start: 0.8404 (tt0) cc_final: 0.8198 (tt0) REVERT: B 180 GLN cc_start: 0.8888 (pp30) cc_final: 0.8618 (pp30) REVERT: B 339 ARG cc_start: 0.8868 (ttp-170) cc_final: 0.8344 (ttm-80) REVERT: B 456 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: B 498 ASP cc_start: 0.8145 (p0) cc_final: 0.7927 (m-30) REVERT: C 174 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7447 (tp30) REVERT: C 178 LYS cc_start: 0.8550 (tmmt) cc_final: 0.8207 (tmmt) REVERT: C 273 CYS cc_start: 0.8859 (m) cc_final: 0.7984 (p) REVERT: C 279 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7725 (mt) REVERT: C 324 GLU cc_start: 0.8811 (tt0) cc_final: 0.8510 (tt0) REVERT: C 337 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.9150 (p) REVERT: C 339 ARG cc_start: 0.9069 (ttp80) cc_final: 0.8485 (ttt-90) REVERT: C 370 MET cc_start: 0.9300 (mtt) cc_final: 0.9057 (mtt) REVERT: C 407 LYS cc_start: 0.9000 (tppp) cc_final: 0.8253 (tppt) REVERT: C 411 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8647 (mp0) REVERT: C 498 ASP cc_start: 0.9252 (OUTLIER) cc_final: 0.8968 (p0) REVERT: D 164 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8873 (ptp) REVERT: D 174 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8121 (mm-30) REVERT: D 190 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8939 (tm) REVERT: D 211 SER cc_start: 0.9040 (t) cc_final: 0.8695 (p) REVERT: D 247 LYS cc_start: 0.8644 (mppt) cc_final: 0.8353 (mmtm) REVERT: D 351 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8485 (mp0) REVERT: D 469 LYS cc_start: 0.9239 (ptmm) cc_final: 0.8882 (ptmm) REVERT: D 479 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7702 (mtp-110) REVERT: E 180 GLN cc_start: 0.9078 (pm20) cc_final: 0.8629 (pm20) REVERT: E 186 PHE cc_start: 0.8695 (m-10) cc_final: 0.8285 (m-80) REVERT: E 191 GLN cc_start: 0.9276 (tt0) cc_final: 0.8639 (tt0) REVERT: E 193 MET cc_start: 0.8657 (tpt) cc_final: 0.8347 (tpp) REVERT: E 197 GLN cc_start: 0.9024 (mm110) cc_final: 0.8732 (mm-40) REVERT: E 206 ARG cc_start: 0.7395 (tpm170) cc_final: 0.6886 (tpm170) REVERT: E 213 ILE cc_start: 0.9182 (pt) cc_final: 0.8961 (pp) REVERT: E 324 GLU cc_start: 0.8910 (tp30) cc_final: 0.8475 (mm-30) REVERT: E 344 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8576 (t0) REVERT: E 412 MET cc_start: 0.9080 (mtm) cc_final: 0.8723 (mtm) REVERT: E 445 ASP cc_start: 0.9033 (t0) cc_final: 0.8525 (t0) REVERT: E 495 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8601 (pt0) REVERT: E 498 ASP cc_start: 0.8525 (t0) cc_final: 0.7966 (t0) REVERT: F 197 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8824 (mt0) REVERT: F 209 GLU cc_start: 0.8485 (mp0) cc_final: 0.8263 (mp0) REVERT: F 242 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9166 (mtpt) REVERT: F 245 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8285 (mppt) REVERT: F 294 MET cc_start: 0.9397 (tpp) cc_final: 0.9155 (mmm) REVERT: F 343 LYS cc_start: 0.9447 (tppp) cc_final: 0.9241 (tppp) REVERT: F 345 CYS cc_start: 0.9030 (m) cc_final: 0.8685 (m) REVERT: F 351 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: F 385 SER cc_start: 0.8926 (OUTLIER) cc_final: 0.8676 (p) outliers start: 99 outliers final: 39 residues processed: 406 average time/residue: 0.6757 time to fit residues: 302.7359 Evaluate side-chains 348 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 290 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 472 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 80 optimal weight: 10.0000 chunk 2 optimal weight: 50.0000 chunk 169 optimal weight: 40.0000 chunk 117 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 127 optimal weight: 0.0040 chunk 70 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 overall best weight: 2.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 ASN D 450 GLN E 202 GLN E 314 GLN ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 GLN F 252 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.080001 restraints weight = 41631.641| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.22 r_work: 0.2893 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.9566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18676 Z= 0.138 Angle : 0.686 14.947 25370 Z= 0.333 Chirality : 0.046 0.173 3010 Planarity : 0.005 0.087 3364 Dihedral : 6.161 80.884 2845 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.73 % Allowed : 29.84 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.17), residues: 2520 helix: 2.03 (0.16), residues: 1150 sheet: -0.35 (0.22), residues: 524 loop : -0.10 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 347 TYR 0.024 0.002 TYR B 486 PHE 0.026 0.001 PHE A 243 TRP 0.008 0.001 TRP A 481 HIS 0.002 0.000 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00333 (18676) covalent geometry : angle 0.68603 (25370) hydrogen bonds : bond 0.02850 ( 1004) hydrogen bonds : angle 3.91095 ( 2937) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 323 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8349 (tm) REVERT: A 202 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8530 (tm-30) REVERT: A 242 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8694 (mtmt) REVERT: A 243 PHE cc_start: 0.8831 (t80) cc_final: 0.8518 (t80) REVERT: A 244 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.6926 (pttm) REVERT: A 247 LYS cc_start: 0.8463 (pmmt) cc_final: 0.8051 (mppt) REVERT: A 324 GLU cc_start: 0.8776 (tt0) cc_final: 0.8105 (tt0) REVERT: A 347 ARG cc_start: 0.8652 (ttm110) cc_final: 0.8208 (mtp85) REVERT: A 398 THR cc_start: 0.9413 (m) cc_final: 0.9103 (p) REVERT: A 407 LYS cc_start: 0.9153 (tppp) cc_final: 0.8913 (tppp) REVERT: A 438 GLU cc_start: 0.8087 (mp0) cc_final: 0.7857 (mp0) REVERT: A 440 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8532 (m) REVERT: A 463 HIS cc_start: 0.8620 (m90) cc_final: 0.8323 (m90) REVERT: A 482 ASP cc_start: 0.9284 (t0) cc_final: 0.9049 (p0) REVERT: B 162 ASP cc_start: 0.7939 (m-30) cc_final: 0.7522 (m-30) REVERT: B 174 GLU cc_start: 0.8440 (tt0) cc_final: 0.8064 (tt0) REVERT: B 180 GLN cc_start: 0.8853 (pp30) cc_final: 0.8502 (pp30) REVERT: B 339 ARG cc_start: 0.8828 (ttp-170) cc_final: 0.8312 (ttm-80) REVERT: B 343 LYS cc_start: 0.9081 (mttp) cc_final: 0.8765 (mmtp) REVERT: B 456 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: C 148 TYR cc_start: 0.8856 (m-80) cc_final: 0.8025 (m-80) REVERT: C 202 GLN cc_start: 0.9197 (mt0) cc_final: 0.8661 (mt0) REVERT: C 244 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8593 (mmpt) REVERT: C 273 CYS cc_start: 0.8839 (m) cc_final: 0.7966 (p) REVERT: C 279 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7690 (mt) REVERT: C 324 GLU cc_start: 0.8842 (tt0) cc_final: 0.8526 (tt0) REVERT: C 339 ARG cc_start: 0.9067 (ttp80) cc_final: 0.8842 (ttm-80) REVERT: C 370 MET cc_start: 0.9288 (mtt) cc_final: 0.9055 (mtt) REVERT: C 407 LYS cc_start: 0.8995 (tppp) cc_final: 0.8252 (tppt) REVERT: C 411 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8657 (mp0) REVERT: C 498 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.8954 (p0) REVERT: D 164 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8799 (ptp) REVERT: D 174 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8180 (mm-30) REVERT: D 178 LYS cc_start: 0.8649 (tmmt) cc_final: 0.8304 (pptt) REVERT: D 190 LEU cc_start: 0.9202 (mm) cc_final: 0.8958 (tm) REVERT: D 202 GLN cc_start: 0.8785 (tt0) cc_final: 0.7949 (tm-30) REVERT: D 211 SER cc_start: 0.9079 (t) cc_final: 0.8763 (p) REVERT: D 351 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8441 (mp0) REVERT: D 469 LYS cc_start: 0.9217 (ptmm) cc_final: 0.8869 (ptmm) REVERT: D 479 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7616 (mtp-110) REVERT: E 164 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8924 (mpt) REVERT: E 180 GLN cc_start: 0.9075 (pm20) cc_final: 0.8587 (pm20) REVERT: E 186 PHE cc_start: 0.8612 (m-10) cc_final: 0.8245 (m-80) REVERT: E 191 GLN cc_start: 0.9265 (tt0) cc_final: 0.8668 (tt0) REVERT: E 213 ILE cc_start: 0.9180 (pt) cc_final: 0.8952 (pp) REVERT: E 324 GLU cc_start: 0.8836 (tp30) cc_final: 0.8396 (mm-30) REVERT: E 378 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.7353 (mpp) REVERT: E 445 ASP cc_start: 0.9096 (t0) cc_final: 0.8601 (t0) REVERT: E 450 GLN cc_start: 0.8691 (pt0) cc_final: 0.8464 (pm20) REVERT: E 498 ASP cc_start: 0.8544 (t0) cc_final: 0.8000 (t0) REVERT: F 197 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8862 (mt0) REVERT: F 209 GLU cc_start: 0.8372 (mp0) cc_final: 0.8123 (mp0) REVERT: F 345 CYS cc_start: 0.9050 (m) cc_final: 0.8708 (m) REVERT: F 351 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: F 385 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8654 (p) REVERT: F 427 ARG cc_start: 0.8927 (mtm110) cc_final: 0.8385 (ptp90) REVERT: F 469 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9106 (tmmm) outliers start: 84 outliers final: 38 residues processed: 384 average time/residue: 0.7150 time to fit residues: 302.1665 Evaluate side-chains 346 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 292 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 378 MET Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 469 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 193 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 213 optimal weight: 50.0000 chunk 21 optimal weight: 4.9990 chunk 240 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 17 optimal weight: 30.0000 chunk 236 optimal weight: 7.9990 chunk 202 optimal weight: 0.2980 chunk 228 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 GLN C 314 GLN E 202 GLN E 314 GLN E 344 ASN F 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.100336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.078168 restraints weight = 41356.195| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.20 r_work: 0.2881 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.9919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18676 Z= 0.179 Angle : 0.708 12.702 25370 Z= 0.346 Chirality : 0.047 0.175 3010 Planarity : 0.005 0.068 3364 Dihedral : 6.215 82.769 2845 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.12 % Allowed : 29.22 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.17), residues: 2520 helix: 2.04 (0.16), residues: 1148 sheet: -0.38 (0.21), residues: 536 loop : -0.08 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 347 TYR 0.032 0.002 TYR E 486 PHE 0.039 0.001 PHE D 243 TRP 0.008 0.001 TRP A 481 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00429 (18676) covalent geometry : angle 0.70753 (25370) hydrogen bonds : bond 0.02953 ( 1004) hydrogen bonds : angle 3.95752 ( 2937) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 307 time to evaluate : 0.474 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: A 192 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8331 (tm) REVERT: A 202 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8592 (tm-30) REVERT: A 215 ASP cc_start: 0.8743 (t0) cc_final: 0.8411 (t0) REVERT: A 243 PHE cc_start: 0.8967 (t80) cc_final: 0.8755 (t80) REVERT: A 247 LYS cc_start: 0.8872 (pmmt) cc_final: 0.8446 (mppt) REVERT: A 324 GLU cc_start: 0.8822 (tt0) cc_final: 0.8170 (tt0) REVERT: A 347 ARG cc_start: 0.8711 (ttm110) cc_final: 0.8322 (mtp85) REVERT: A 351 GLU cc_start: 0.8977 (mp0) cc_final: 0.8654 (mp0) REVERT: A 398 THR cc_start: 0.9439 (m) cc_final: 0.9131 (p) REVERT: A 438 GLU cc_start: 0.8184 (mp0) cc_final: 0.7974 (mp0) REVERT: A 463 HIS cc_start: 0.8665 (m90) cc_final: 0.8325 (m90) REVERT: A 482 ASP cc_start: 0.9314 (t0) cc_final: 0.9084 (p0) REVERT: B 158 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8320 (t0) REVERT: B 162 ASP cc_start: 0.8021 (m-30) cc_final: 0.7682 (m-30) REVERT: B 180 GLN cc_start: 0.8823 (pp30) cc_final: 0.8559 (pp30) REVERT: B 339 ARG cc_start: 0.8882 (ttp-170) cc_final: 0.8587 (ttm-80) REVERT: B 343 LYS cc_start: 0.9079 (mttp) cc_final: 0.8865 (mmtp) REVERT: B 450 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8597 (pt0) REVERT: B 456 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: C 148 TYR cc_start: 0.8891 (m-80) cc_final: 0.8060 (m-80) REVERT: C 164 MET cc_start: 0.9331 (mtm) cc_final: 0.9067 (mpp) REVERT: C 174 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: C 202 GLN cc_start: 0.9103 (mt0) cc_final: 0.8574 (mt0) REVERT: C 273 CYS cc_start: 0.8823 (m) cc_final: 0.7935 (p) REVERT: C 324 GLU cc_start: 0.8812 (tt0) cc_final: 0.8504 (tt0) REVERT: C 339 ARG cc_start: 0.9111 (ttp80) cc_final: 0.8801 (ttm-80) REVERT: C 370 MET cc_start: 0.9318 (mtt) cc_final: 0.9109 (mtt) REVERT: C 407 LYS cc_start: 0.9007 (tppp) cc_final: 0.8286 (tppt) REVERT: C 411 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8683 (mp0) REVERT: C 498 ASP cc_start: 0.9257 (OUTLIER) cc_final: 0.9011 (p0) REVERT: D 164 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8861 (ptp) REVERT: D 174 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8199 (mm-30) REVERT: D 190 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8997 (tm) REVERT: D 193 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8694 (tpt) REVERT: D 202 GLN cc_start: 0.8798 (tt0) cc_final: 0.7999 (tm-30) REVERT: D 211 SER cc_start: 0.9036 (t) cc_final: 0.8717 (p) REVERT: D 351 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8510 (mp0) REVERT: D 469 LYS cc_start: 0.9174 (ptmm) cc_final: 0.8828 (ptmm) REVERT: D 479 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7859 (mtp-110) REVERT: E 180 GLN cc_start: 0.9056 (pm20) cc_final: 0.8717 (pm20) REVERT: E 186 PHE cc_start: 0.8737 (m-10) cc_final: 0.8299 (m-80) REVERT: E 191 GLN cc_start: 0.9277 (tt0) cc_final: 0.8639 (tt0) REVERT: E 213 ILE cc_start: 0.9192 (pt) cc_final: 0.8972 (pp) REVERT: E 324 GLU cc_start: 0.8827 (tp30) cc_final: 0.8374 (mm-30) REVERT: E 344 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8456 (t0) REVERT: E 378 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.7407 (mpp) REVERT: E 445 ASP cc_start: 0.9112 (t0) cc_final: 0.8579 (t0) REVERT: E 450 GLN cc_start: 0.8704 (pt0) cc_final: 0.8462 (pm20) REVERT: E 498 ASP cc_start: 0.8672 (t0) cc_final: 0.8166 (t0) REVERT: F 197 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8889 (mt0) REVERT: F 242 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9141 (mtpt) REVERT: F 351 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: F 385 SER cc_start: 0.8926 (OUTLIER) cc_final: 0.8651 (p) REVERT: F 427 ARG cc_start: 0.8970 (mtm110) cc_final: 0.8461 (ptp90) outliers start: 91 outliers final: 41 residues processed: 375 average time/residue: 0.6890 time to fit residues: 284.3244 Evaluate side-chains 336 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 278 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 378 MET Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 472 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 101 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 214 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 172 optimal weight: 30.0000 chunk 193 optimal weight: 0.0570 chunk 118 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 143 optimal weight: 0.7980 overall best weight: 3.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 GLN C 180 GLN C 314 GLN E 202 GLN E 314 GLN ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.100569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.078812 restraints weight = 41302.829| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.18 r_work: 0.2862 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 1.0091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18676 Z= 0.153 Angle : 0.723 18.900 25370 Z= 0.352 Chirality : 0.047 0.198 3010 Planarity : 0.005 0.066 3364 Dihedral : 6.151 82.524 2845 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.05 % Allowed : 30.63 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.17), residues: 2520 helix: 2.01 (0.16), residues: 1148 sheet: -0.28 (0.21), residues: 526 loop : -0.11 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 491 TYR 0.029 0.002 TYR B 486 PHE 0.027 0.001 PHE A 243 TRP 0.007 0.001 TRP F 481 HIS 0.002 0.000 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00372 (18676) covalent geometry : angle 0.72285 (25370) hydrogen bonds : bond 0.02912 ( 1004) hydrogen bonds : angle 3.92799 ( 2937) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 294 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8272 (tm) REVERT: A 202 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8607 (tm-30) REVERT: A 215 ASP cc_start: 0.8760 (t0) cc_final: 0.8437 (t0) REVERT: A 247 LYS cc_start: 0.8732 (pmmt) cc_final: 0.8420 (mppt) REVERT: A 317 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8741 (mp10) REVERT: A 324 GLU cc_start: 0.8786 (tt0) cc_final: 0.8154 (tt0) REVERT: A 347 ARG cc_start: 0.8709 (ttm110) cc_final: 0.8369 (mtp85) REVERT: A 351 GLU cc_start: 0.8987 (mp0) cc_final: 0.8707 (mp0) REVERT: A 398 THR cc_start: 0.9456 (m) cc_final: 0.9122 (p) REVERT: A 399 MET cc_start: 0.8917 (pp-130) cc_final: 0.8710 (pp-130) REVERT: A 411 GLU cc_start: 0.8445 (pt0) cc_final: 0.7816 (pm20) REVERT: A 463 HIS cc_start: 0.8679 (m90) cc_final: 0.8313 (m90) REVERT: A 482 ASP cc_start: 0.9301 (t0) cc_final: 0.9092 (p0) REVERT: B 158 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8356 (t0) REVERT: B 162 ASP cc_start: 0.8050 (m-30) cc_final: 0.7416 (m-30) REVERT: B 174 GLU cc_start: 0.8538 (tt0) cc_final: 0.7775 (mt-10) REVERT: B 180 GLN cc_start: 0.8777 (pp30) cc_final: 0.8401 (pp30) REVERT: B 206 ARG cc_start: 0.8315 (mmm160) cc_final: 0.7960 (tpp-160) REVERT: B 339 ARG cc_start: 0.8864 (ttp-170) cc_final: 0.8465 (ttm-80) REVERT: B 343 LYS cc_start: 0.9131 (mttp) cc_final: 0.8918 (mmtp) REVERT: B 456 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: C 148 TYR cc_start: 0.8913 (m-80) cc_final: 0.8062 (m-80) REVERT: C 164 MET cc_start: 0.9344 (mtm) cc_final: 0.9070 (mpp) REVERT: C 174 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7621 (tp30) REVERT: C 178 LYS cc_start: 0.8610 (tmmt) cc_final: 0.7963 (pptt) REVERT: C 180 GLN cc_start: 0.9055 (pt0) cc_final: 0.8832 (pt0) REVERT: C 202 GLN cc_start: 0.9122 (mt0) cc_final: 0.8543 (mt0) REVERT: C 273 CYS cc_start: 0.8803 (m) cc_final: 0.7925 (p) REVERT: C 324 GLU cc_start: 0.8792 (tt0) cc_final: 0.8432 (tt0) REVERT: C 339 ARG cc_start: 0.9076 (ttp80) cc_final: 0.8654 (tpt-90) REVERT: C 370 MET cc_start: 0.9316 (mtt) cc_final: 0.9109 (mtt) REVERT: C 407 LYS cc_start: 0.9032 (tppp) cc_final: 0.8317 (tppt) REVERT: C 411 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8696 (mp0) REVERT: C 498 ASP cc_start: 0.9278 (OUTLIER) cc_final: 0.8999 (p0) REVERT: D 174 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7999 (mm-30) REVERT: D 178 LYS cc_start: 0.8638 (tmmt) cc_final: 0.8298 (pptt) REVERT: D 190 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8992 (tm) REVERT: D 193 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8749 (tpt) REVERT: D 202 GLN cc_start: 0.8802 (tt0) cc_final: 0.8002 (tm-30) REVERT: D 351 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8454 (mp0) REVERT: D 469 LYS cc_start: 0.9159 (ptmm) cc_final: 0.8825 (ptmm) REVERT: D 479 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7690 (mtp-110) REVERT: E 180 GLN cc_start: 0.9059 (pm20) cc_final: 0.8740 (pm20) REVERT: E 186 PHE cc_start: 0.8730 (m-10) cc_final: 0.8310 (m-80) REVERT: E 191 GLN cc_start: 0.9285 (tt0) cc_final: 0.8676 (tt0) REVERT: E 213 ILE cc_start: 0.9202 (pt) cc_final: 0.8980 (pp) REVERT: E 227 ILE cc_start: 0.8935 (mm) cc_final: 0.8734 (tp) REVERT: E 238 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8968 (mm) REVERT: E 324 GLU cc_start: 0.8928 (tp30) cc_final: 0.8532 (mm-30) REVERT: E 412 MET cc_start: 0.9231 (mtp) cc_final: 0.8877 (mtp) REVERT: E 445 ASP cc_start: 0.9099 (t0) cc_final: 0.8593 (t0) REVERT: E 450 GLN cc_start: 0.8694 (pt0) cc_final: 0.8439 (pm20) REVERT: E 498 ASP cc_start: 0.8694 (t0) cc_final: 0.8192 (t0) REVERT: F 242 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9132 (mtpt) REVERT: F 351 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: F 385 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8680 (p) REVERT: F 427 ARG cc_start: 0.8999 (mtm110) cc_final: 0.8490 (ptp90) outliers start: 72 outliers final: 33 residues processed: 346 average time/residue: 0.7501 time to fit residues: 286.4706 Evaluate side-chains 327 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 472 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 191 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 49 optimal weight: 0.0060 chunk 197 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 overall best weight: 4.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 ASN B 450 GLN C 314 GLN E 202 GLN E 314 GLN E 344 ASN F 314 GLN F 470 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.099987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.078316 restraints weight = 41207.173| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.15 r_work: 0.2855 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 1.0328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18676 Z= 0.173 Angle : 0.727 16.063 25370 Z= 0.354 Chirality : 0.047 0.208 3010 Planarity : 0.005 0.079 3364 Dihedral : 6.174 85.279 2845 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.21 % Allowed : 31.42 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.17), residues: 2520 helix: 1.99 (0.16), residues: 1150 sheet: -0.30 (0.21), residues: 528 loop : -0.08 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 491 TYR 0.028 0.002 TYR E 486 PHE 0.039 0.002 PHE D 243 TRP 0.005 0.001 TRP F 481 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00421 (18676) covalent geometry : angle 0.72702 (25370) hydrogen bonds : bond 0.02932 ( 1004) hydrogen bonds : angle 3.94497 ( 2937) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.9219 (pt0) cc_final: 0.8818 (mp10) REVERT: A 192 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8321 (tm) REVERT: A 202 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8604 (tm-30) REVERT: A 324 GLU cc_start: 0.8807 (tt0) cc_final: 0.8220 (tt0) REVERT: A 347 ARG cc_start: 0.8729 (ttm110) cc_final: 0.8430 (mtp85) REVERT: A 351 GLU cc_start: 0.8992 (mp0) cc_final: 0.8700 (mp0) REVERT: A 398 THR cc_start: 0.9496 (m) cc_final: 0.9136 (p) REVERT: A 407 LYS cc_start: 0.9188 (tptp) cc_final: 0.8918 (tppt) REVERT: A 463 HIS cc_start: 0.8778 (m90) cc_final: 0.8450 (m90) REVERT: B 158 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8414 (t0) REVERT: B 162 ASP cc_start: 0.8012 (m-30) cc_final: 0.7440 (m-30) REVERT: B 174 GLU cc_start: 0.8446 (tt0) cc_final: 0.7777 (mt-10) REVERT: B 206 ARG cc_start: 0.8209 (mmm160) cc_final: 0.7947 (tpp-160) REVERT: B 343 LYS cc_start: 0.9116 (mttp) cc_final: 0.8875 (mmtp) REVERT: B 491 ARG cc_start: 0.8607 (tmm-80) cc_final: 0.8371 (ttp80) REVERT: C 148 TYR cc_start: 0.8922 (m-80) cc_final: 0.8174 (m-10) REVERT: C 164 MET cc_start: 0.9375 (mtm) cc_final: 0.8967 (mpp) REVERT: C 174 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: C 202 GLN cc_start: 0.9125 (mt0) cc_final: 0.8744 (mt0) REVERT: C 256 PHE cc_start: 0.9102 (m-10) cc_final: 0.8901 (m-10) REVERT: C 273 CYS cc_start: 0.8792 (m) cc_final: 0.7902 (p) REVERT: C 324 GLU cc_start: 0.8748 (tt0) cc_final: 0.8380 (tt0) REVERT: C 339 ARG cc_start: 0.9078 (ttp80) cc_final: 0.8714 (tpt-90) REVERT: C 407 LYS cc_start: 0.9059 (tppp) cc_final: 0.8294 (tppt) REVERT: C 411 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8669 (mp0) REVERT: D 174 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: D 178 LYS cc_start: 0.8666 (tmmt) cc_final: 0.8337 (pptt) REVERT: D 190 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.9004 (tm) REVERT: D 193 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8756 (tpt) REVERT: D 202 GLN cc_start: 0.8816 (tt0) cc_final: 0.8025 (tm-30) REVERT: D 351 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8491 (mp0) REVERT: D 469 LYS cc_start: 0.9169 (ptmm) cc_final: 0.8849 (ptmm) REVERT: D 479 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7864 (mtp-110) REVERT: E 180 GLN cc_start: 0.9060 (pm20) cc_final: 0.8729 (pm20) REVERT: E 186 PHE cc_start: 0.8821 (m-10) cc_final: 0.8455 (m-80) REVERT: E 191 GLN cc_start: 0.9301 (tt0) cc_final: 0.8686 (tt0) REVERT: E 213 ILE cc_start: 0.9229 (pt) cc_final: 0.9013 (pp) REVERT: E 227 ILE cc_start: 0.8992 (mm) cc_final: 0.8773 (tp) REVERT: E 324 GLU cc_start: 0.8933 (tp30) cc_final: 0.8528 (mm-30) REVERT: E 344 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8467 (t0) REVERT: E 412 MET cc_start: 0.9313 (mtp) cc_final: 0.8943 (mtp) REVERT: E 445 ASP cc_start: 0.9027 (t0) cc_final: 0.8501 (t0) REVERT: E 498 ASP cc_start: 0.8750 (t0) cc_final: 0.8246 (OUTLIER) REVERT: F 242 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9195 (mtpt) REVERT: F 324 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8122 (mm-30) REVERT: F 351 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: F 384 ASN cc_start: 0.9166 (m-40) cc_final: 0.8908 (m110) REVERT: F 385 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8694 (p) REVERT: F 427 ARG cc_start: 0.9005 (mtm110) cc_final: 0.8529 (ptp90) outliers start: 57 outliers final: 31 residues processed: 331 average time/residue: 0.7684 time to fit residues: 279.9330 Evaluate side-chains 307 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 472 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 48 optimal weight: 50.0000 chunk 70 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 226 optimal weight: 6.9990 chunk 207 optimal weight: 40.0000 chunk 119 optimal weight: 7.9990 chunk 114 optimal weight: 0.3980 chunk 237 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 213 optimal weight: 50.0000 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 GLN E 202 GLN E 450 GLN F 225 ASN F 314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.097278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.074697 restraints weight = 40885.435| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.10 r_work: 0.2847 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 1.0349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 18676 Z= 0.277 Angle : 1.002 59.178 25370 Z= 0.586 Chirality : 0.052 1.107 3010 Planarity : 0.006 0.115 3364 Dihedral : 6.207 85.283 2845 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.82 % Allowed : 31.98 % Favored : 65.20 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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: 1.15 (0.17), residues: 2520 helix: 1.96 (0.16), residues: 1150 sheet: -0.29 (0.21), residues: 528 loop : -0.09 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 491 TYR 0.017 0.002 TYR E 486 PHE 0.031 0.002 PHE A 243 TRP 0.004 0.001 TRP F 481 HIS 0.139 0.003 HIS F 470 Details of bonding type rmsd covalent geometry : bond 0.00547 (18676) covalent geometry : angle 1.00184 (25370) hydrogen bonds : bond 0.03005 ( 1004) hydrogen bonds : angle 3.95938 ( 2937) =============================================================================== Job complete usr+sys time: 7534.65 seconds wall clock time: 128 minutes 49.22 seconds (7729.22 seconds total)