Starting phenix.real_space_refine on Sun Aug 24 14:59:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1m_39730/08_2025/8z1m_39730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1m_39730/08_2025/8z1m_39730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z1m_39730/08_2025/8z1m_39730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1m_39730/08_2025/8z1m_39730.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1m_39730/08_2025/8z1m_39730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1m_39730/08_2025/8z1m_39730.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 13062 2.51 5 N 3600 2.21 5 O 3960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20694 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3449 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 441} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3449 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 441} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3449 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 441} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3449 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 441} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3449 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 441} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3449 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 441} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 4.96, per 1000 atoms: 0.24 Number of scatterers: 20694 At special positions: 0 Unit cell: (115.56, 117.7, 118.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3960 8.00 N 3600 7.00 C 13062 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: 1.61 Conformation dependent library (CDL) restraints added in 860.9 milliseconds Enol-peptide restraints added in 1.4 microseconds 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 14 sheets defined 54.1% alpha, 9.0% 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 7 through 24 Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.514A pdb=" N LYS A 29 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 42 removed outlier: 3.749A pdb=" N ALA A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 107 removed outlier: 3.956A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 141 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 195 through 214 Processing helix chain 'A' and resid 230 through 244 Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.510A pdb=" N VAL A 310 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'A' and resid 350 through 364 removed outlier: 3.635A pdb=" N GLU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 364 " --> pdb=" O HIS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 379 through 396 removed outlier: 4.420A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 426 Processing helix chain 'A' and resid 436 through 456 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.825A pdb=" N LYS B 29 " --> pdb=" O THR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 41 removed outlier: 3.620A pdb=" N ALA B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 107 removed outlier: 3.934A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 141 Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 158 through 174 Processing helix chain 'B' and resid 196 through 213 removed outlier: 3.676A pdb=" N VAL B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 Processing helix chain 'B' and resid 268 through 278 Processing helix chain 'B' and resid 284 through 291 removed outlier: 3.530A pdb=" N ASP B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 295 Processing helix chain 'B' and resid 326 through 337 removed outlier: 4.150A pdb=" N ILE B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 335 " --> pdb=" O GLN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.891A pdb=" N ILE B 354 " --> pdb=" O THR B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 396 removed outlier: 3.716A pdb=" N ALA B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 426 Processing helix chain 'B' and resid 436 through 456 removed outlier: 3.680A pdb=" N GLY B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 446 " --> pdb=" O ASN B 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 25 through 30 removed outlier: 3.541A pdb=" N LYS C 29 " --> pdb=" O THR C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 42 removed outlier: 3.655A pdb=" N ALA C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 107 removed outlier: 3.956A pdb=" N PHE C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 141 Processing helix chain 'C' and resid 158 through 174 Processing helix chain 'C' and resid 195 through 214 Processing helix chain 'C' and resid 230 through 244 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 285 through 290 removed outlier: 3.616A pdb=" N VAL C 289 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 296 removed outlier: 4.134A pdb=" N ASP C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 326 through 337 Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 357 through 364 Processing helix chain 'C' and resid 374 through 379 Processing helix chain 'C' and resid 379 through 396 removed outlier: 4.380A pdb=" N VAL C 383 " --> pdb=" O ASN C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 426 Processing helix chain 'C' and resid 436 through 456 removed outlier: 3.671A pdb=" N GLY C 440 " --> pdb=" O SER C 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 24 Processing helix chain 'D' and resid 32 through 42 removed outlier: 3.748A pdb=" N ALA D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL D 42 " --> pdb=" O ALA D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 107 removed outlier: 3.966A pdb=" N PHE D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 141 Processing helix chain 'D' and resid 158 through 174 Processing helix chain 'D' and resid 196 through 213 removed outlier: 4.094A pdb=" N VAL D 202 " --> pdb=" O GLY D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 243 Processing helix chain 'D' and resid 268 through 281 Processing helix chain 'D' and resid 283 through 291 removed outlier: 3.599A pdb=" N LEU D 288 " --> pdb=" O GLN D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 297 Processing helix chain 'D' and resid 305 through 309 Processing helix chain 'D' and resid 326 through 336 Processing helix chain 'D' and resid 350 through 362 removed outlier: 3.680A pdb=" N ILE D 354 " --> pdb=" O THR D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 379 Processing helix chain 'D' and resid 380 through 396 Processing helix chain 'D' and resid 400 through 426 Processing helix chain 'D' and resid 436 through 456 Processing helix chain 'F' and resid 7 through 23 Processing helix chain 'F' and resid 32 through 42 removed outlier: 3.649A pdb=" N ALA F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA F 38 " --> pdb=" O ARG F 34 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 107 removed outlier: 3.926A pdb=" N PHE F 101 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 107 " --> pdb=" O ASN F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 141 Processing helix chain 'F' and resid 158 through 174 Processing helix chain 'F' and resid 195 through 214 Processing helix chain 'F' and resid 230 through 244 Processing helix chain 'F' and resid 268 through 281 Processing helix chain 'F' and resid 285 through 290 Processing helix chain 'F' and resid 291 through 297 Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'F' and resid 326 through 337 Processing helix chain 'F' and resid 350 through 364 Processing helix chain 'F' and resid 374 through 379 Processing helix chain 'F' and resid 380 through 396 Processing helix chain 'F' and resid 400 through 426 Processing helix chain 'F' and resid 436 through 456 Processing helix chain 'E' and resid 7 through 24 Processing helix chain 'E' and resid 25 through 30 removed outlier: 3.706A pdb=" N LYS E 29 " --> pdb=" O THR E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 41 removed outlier: 3.711A pdb=" N ALA E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 107 removed outlier: 3.946A pdb=" N PHE E 101 " --> pdb=" O PHE E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 141 Processing helix chain 'E' and resid 158 through 174 Processing helix chain 'E' and resid 196 through 213 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 268 through 281 removed outlier: 3.782A pdb=" N ASP E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 306 through 310 removed outlier: 3.824A pdb=" N VAL E 310 " --> pdb=" O TRP E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 337 Processing helix chain 'E' and resid 350 through 364 removed outlier: 3.991A pdb=" N GLU E 358 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 369 Processing helix chain 'E' and resid 379 through 396 removed outlier: 4.425A pdb=" N VAL E 383 " --> pdb=" O ASN E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 427 Processing helix chain 'E' and resid 436 through 456 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 152 removed outlier: 5.753A pdb=" N LYS A 78 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLY A 115 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLY A 80 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER A 117 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG A 82 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY A 112 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLU A 59 " --> pdb=" O ASN A 55 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 55 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY D 112 " --> pdb=" O PHE D 70 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLY D 80 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER D 117 " --> pdb=" O GLY D 80 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG D 82 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 245 through 247 removed outlier: 6.180A pdb=" N LYS A 222 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG A 223 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LEU A 317 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA A 225 " --> pdb=" O LEU A 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 340 through 342 removed outlier: 7.670A pdb=" N ILE A 341 " --> pdb=" O ALA A 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 149 through 152 removed outlier: 5.693A pdb=" N LYS B 78 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLY B 115 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY B 80 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER B 117 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG B 82 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY B 112 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY F 112 " --> pdb=" O PHE F 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 257 through 259 Processing sheet with id=AA6, first strand: chain 'B' and resid 315 through 316 removed outlier: 6.130A pdb=" N ALA B 316 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 6.295A pdb=" N ARG C 82 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY C 112 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN E 55 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU E 59 " --> pdb=" O ASN E 55 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY E 112 " --> pdb=" O PHE E 70 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LYS E 78 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLY E 115 " --> pdb=" O LYS E 78 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLY E 80 " --> pdb=" O GLY E 115 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER E 117 " --> pdb=" O GLY E 80 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ARG E 82 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 246 through 247 removed outlier: 5.679A pdb=" N ARG C 246 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 315 " --> pdb=" O ARG C 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 256 through 259 Processing sheet with id=AB1, first strand: chain 'D' and resid 246 through 247 removed outlier: 6.269A pdb=" N ARG D 246 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ARG D 223 " --> pdb=" O VAL D 315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 256 through 259 removed outlier: 3.502A pdb=" N LEU D 301 " --> pdb=" O SER D 256 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 223 through 224 removed outlier: 5.857A pdb=" N ARG F 246 " --> pdb=" O VAL F 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 249 through 250 removed outlier: 3.590A pdb=" N LEU F 250 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE F 258 " --> pdb=" O THR F 299 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 249 through 251 removed outlier: 3.565A pdb=" N ILE E 258 " --> pdb=" O THR E 299 " (cutoff:3.500A) 1153 hydrogen bonds defined for protein. 3390 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: 3.79 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3711 1.31 - 1.45: 6007 1.45 - 1.58: 11282 1.58 - 1.72: 0 1.72 - 1.85: 114 Bond restraints: 21114 Sorted by residual: bond pdb=" N GLN D 254 " pdb=" CA GLN D 254 " ideal model delta sigma weight residual 1.458 1.490 -0.031 6.30e-03 2.52e+04 2.47e+01 bond pdb=" C LYS D 114 " pdb=" O LYS D 114 " ideal model delta sigma weight residual 1.235 1.177 0.059 1.26e-02 6.30e+03 2.17e+01 bond pdb=" C LYS E 114 " pdb=" O LYS E 114 " ideal model delta sigma weight residual 1.235 1.178 0.058 1.26e-02 6.30e+03 2.09e+01 bond pdb=" CE1 HIS A 143 " pdb=" NE2 HIS A 143 " ideal model delta sigma weight residual 1.321 1.278 0.043 1.00e-02 1.00e+04 1.85e+01 bond pdb=" C LYS A 114 " pdb=" O LYS A 114 " ideal model delta sigma weight residual 1.235 1.181 0.054 1.26e-02 6.30e+03 1.84e+01 ... (remaining 21109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 26828 2.03 - 4.06: 1625 4.06 - 6.09: 102 6.09 - 8.12: 25 8.12 - 10.15: 4 Bond angle restraints: 28584 Sorted by residual: angle pdb=" OE1 GLN E 48 " pdb=" CD GLN E 48 " pdb=" NE2 GLN E 48 " ideal model delta sigma weight residual 122.60 129.56 -6.96 1.00e+00 1.00e+00 4.85e+01 angle pdb=" OE1 GLN D 48 " pdb=" CD GLN D 48 " pdb=" NE2 GLN D 48 " ideal model delta sigma weight residual 122.60 127.78 -5.18 1.00e+00 1.00e+00 2.68e+01 angle pdb=" CB ARG F 170 " pdb=" CG ARG F 170 " pdb=" CD ARG F 170 " ideal model delta sigma weight residual 111.30 101.15 10.15 2.30e+00 1.89e-01 1.95e+01 angle pdb=" CA ASP A 154 " pdb=" CB ASP A 154 " pdb=" CG ASP A 154 " ideal model delta sigma weight residual 112.60 116.92 -4.32 1.00e+00 1.00e+00 1.87e+01 angle pdb=" OD1 ASN A 63 " pdb=" CG ASN A 63 " pdb=" ND2 ASN A 63 " ideal model delta sigma weight residual 122.60 126.91 -4.31 1.00e+00 1.00e+00 1.86e+01 ... (remaining 28579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 10743 17.82 - 35.64: 1269 35.64 - 53.46: 306 53.46 - 71.28: 87 71.28 - 89.10: 39 Dihedral angle restraints: 12444 sinusoidal: 4734 harmonic: 7710 Sorted by residual: dihedral pdb=" C ARG F 50 " pdb=" N ARG F 50 " pdb=" CA ARG F 50 " pdb=" CB ARG F 50 " ideal model delta harmonic sigma weight residual -122.60 -113.16 -9.44 0 2.50e+00 1.60e-01 1.43e+01 dihedral pdb=" CA PRO D 435 " pdb=" C PRO D 435 " pdb=" N SER D 436 " pdb=" CA SER D 436 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" C ARG C 50 " pdb=" N ARG C 50 " pdb=" CA ARG C 50 " pdb=" CB ARG C 50 " ideal model delta harmonic sigma weight residual -122.60 -113.26 -9.34 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 12441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1659 0.053 - 0.106: 968 0.106 - 0.159: 352 0.159 - 0.212: 96 0.212 - 0.265: 33 Chirality restraints: 3108 Sorted by residual: chirality pdb=" CB VAL A 134 " pdb=" CA VAL A 134 " pdb=" CG1 VAL A 134 " pdb=" CG2 VAL A 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA PRO D 76 " pdb=" N PRO D 76 " pdb=" C PRO D 76 " pdb=" CB PRO D 76 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL F 134 " pdb=" CA VAL F 134 " pdb=" CG1 VAL F 134 " pdb=" CG2 VAL F 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3105 not shown) Planarity restraints: 3774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 460 " 0.094 2.00e-02 2.50e+03 5.41e-02 7.33e+01 pdb=" CG TRP B 460 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP B 460 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 460 " -0.061 2.00e-02 2.50e+03 pdb=" NE1 TRP B 460 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TRP B 460 " 0.031 2.00e-02 2.50e+03 pdb=" CE3 TRP B 460 " -0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 460 " 0.095 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 460 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP B 460 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 460 " -0.093 2.00e-02 2.50e+03 5.23e-02 6.84e+01 pdb=" CG TRP A 460 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 460 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP A 460 " 0.057 2.00e-02 2.50e+03 pdb=" NE1 TRP A 460 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TRP A 460 " -0.030 2.00e-02 2.50e+03 pdb=" CE3 TRP A 460 " 0.022 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 460 " -0.096 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 460 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP A 460 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 460 " 0.083 2.00e-02 2.50e+03 4.78e-02 5.72e+01 pdb=" CG TRP E 460 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP E 460 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP E 460 " -0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP E 460 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP E 460 " 0.035 2.00e-02 2.50e+03 pdb=" CE3 TRP E 460 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 460 " 0.085 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 460 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP E 460 " -0.020 2.00e-02 2.50e+03 ... (remaining 3771 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 319 2.65 - 3.21: 19897 3.21 - 3.77: 34401 3.77 - 4.34: 47691 4.34 - 4.90: 78817 Nonbonded interactions: 181125 Sorted by model distance: nonbonded pdb=" OG SER A 175 " pdb=" OE2 GLU A 177 " model vdw 2.084 3.040 nonbonded pdb=" OG SER E 175 " pdb=" OE1 GLU E 177 " model vdw 2.093 3.040 nonbonded pdb=" NE2 GLN E 69 " pdb=" OD2 ASP E 149 " model vdw 2.138 3.120 nonbonded pdb=" O THR E 321 " pdb=" ND2 ASN E 346 " model vdw 2.140 3.120 nonbonded pdb=" OD1 ASP A 154 " pdb=" N ILE A 155 " model vdw 2.140 3.120 ... (remaining 181120 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.110 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 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 : 0.011 0.080 21114 Z= 0.703 Angle : 1.083 10.147 28584 Z= 0.712 Chirality : 0.076 0.265 3108 Planarity : 0.015 0.196 3774 Dihedral : 17.363 89.098 7548 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.96 % Favored : 93.57 % Rotamer: Outliers : 1.20 % Allowed : 20.64 % Favored : 78.16 % 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: 0.11 (0.16), residues: 2736 helix: 1.35 (0.13), residues: 1404 sheet: -0.13 (0.37), residues: 258 loop : -1.63 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.005 ARG F 142 TYR 0.063 0.011 TYR D 164 PHE 0.086 0.009 PHE B 66 TRP 0.096 0.015 TRP A 460 HIS 0.022 0.005 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.01133 (21114) covalent geometry : angle 1.08272 (28584) hydrogen bonds : bond 0.13554 ( 1153) hydrogen bonds : angle 5.50738 ( 3390) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: B 199 TYR cc_start: 0.6440 (m-10) cc_final: 0.6186 (m-10) REVERT: C 139 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6654 (mm-30) REVERT: C 347 MET cc_start: 0.2896 (mmm) cc_final: 0.2634 (mtt) REVERT: D 199 TYR cc_start: 0.6041 (m-10) cc_final: 0.5756 (m-10) REVERT: F 24 SER cc_start: 0.7198 (OUTLIER) cc_final: 0.6912 (p) REVERT: F 139 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6597 (mm-30) REVERT: F 425 GLU cc_start: 0.6703 (tp30) cc_final: 0.6421 (tt0) REVERT: E 396 ARG cc_start: 0.6893 (mtp85) cc_final: 0.6635 (mtt180) outliers start: 25 outliers final: 8 residues processed: 227 average time/residue: 0.1437 time to fit residues: 51.3967 Evaluate side-chains 192 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 183 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain E residue 341 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN C 28 GLN D 254 GLN F 69 GLN E 28 GLN ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.201972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.143314 restraints weight = 22174.822| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.50 r_work: 0.3101 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21114 Z= 0.120 Angle : 0.510 8.032 28584 Z= 0.270 Chirality : 0.040 0.134 3108 Planarity : 0.004 0.059 3774 Dihedral : 4.291 66.252 2956 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.85 % Favored : 93.82 % Rotamer: Outliers : 2.44 % Allowed : 19.59 % Favored : 77.97 % 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: 0.60 (0.17), residues: 2736 helix: 1.86 (0.14), residues: 1386 sheet: -0.30 (0.36), residues: 267 loop : -1.41 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 64 TYR 0.015 0.001 TYR E 235 PHE 0.013 0.002 PHE E 340 TRP 0.009 0.001 TRP A 176 HIS 0.003 0.001 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.00261 (21114) covalent geometry : angle 0.50981 (28584) hydrogen bonds : bond 0.03981 ( 1153) hydrogen bonds : angle 4.51762 ( 3390) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8967 (t80) REVERT: A 193 ARG cc_start: 0.7228 (ttm-80) cc_final: 0.6798 (ttm-80) REVERT: A 343 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6645 (tt0) REVERT: A 347 MET cc_start: 0.4275 (mmm) cc_final: 0.1627 (tpp) REVERT: A 424 LYS cc_start: 0.8007 (tppt) cc_final: 0.7747 (ttpp) REVERT: B 28 GLN cc_start: 0.6468 (pp30) cc_final: 0.6122 (pt0) REVERT: B 70 PHE cc_start: 0.9491 (OUTLIER) cc_final: 0.9141 (t80) REVERT: B 173 ARG cc_start: 0.8457 (mmt90) cc_final: 0.8169 (mmt-90) REVERT: B 208 MET cc_start: 0.7851 (ptm) cc_final: 0.7507 (ptm) REVERT: B 296 ASP cc_start: 0.2410 (OUTLIER) cc_final: 0.1602 (t0) REVERT: B 396 ARG cc_start: 0.8561 (mtp85) cc_final: 0.8186 (mtt180) REVERT: B 442 ASN cc_start: 0.7677 (m-40) cc_final: 0.7391 (m110) REVERT: C 28 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.5952 (mp10) REVERT: C 29 LYS cc_start: 0.6894 (tttp) cc_final: 0.6684 (tttt) REVERT: C 282 ARG cc_start: 0.3663 (OUTLIER) cc_final: 0.3215 (mpp-170) REVERT: D 70 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8951 (t80) REVERT: D 199 TYR cc_start: 0.7588 (m-10) cc_final: 0.7142 (m-10) REVERT: D 254 GLN cc_start: 0.4824 (OUTLIER) cc_final: 0.3855 (mp10) REVERT: D 347 MET cc_start: 0.5320 (mpp) cc_final: 0.4633 (mpp) REVERT: D 396 ARG cc_start: 0.8513 (mtt-85) cc_final: 0.8178 (mtt-85) REVERT: F 139 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7216 (mm-30) REVERT: F 149 ASP cc_start: 0.8377 (m-30) cc_final: 0.8160 (m-30) REVERT: F 317 LEU cc_start: 0.7694 (tt) cc_final: 0.7344 (tt) REVERT: F 379 ASN cc_start: 0.8137 (p0) cc_final: 0.7773 (p0) REVERT: E 247 VAL cc_start: 0.5050 (OUTLIER) cc_final: 0.4727 (p) REVERT: E 347 MET cc_start: 0.4750 (tpp) cc_final: 0.3193 (mtm) REVERT: E 396 ARG cc_start: 0.8535 (mtp85) cc_final: 0.8149 (mtt180) outliers start: 51 outliers final: 20 residues processed: 250 average time/residue: 0.1511 time to fit residues: 57.6432 Evaluate side-chains 221 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 254 GLN Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 28 GLN Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 341 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 20 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 268 optimal weight: 0.5980 chunk 269 optimal weight: 0.8980 chunk 235 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN C 379 ASN D 211 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.201622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.152419 restraints weight = 22268.505| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.58 r_work: 0.3106 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21114 Z= 0.142 Angle : 0.506 7.067 28584 Z= 0.267 Chirality : 0.040 0.163 3108 Planarity : 0.004 0.050 3774 Dihedral : 4.079 59.259 2944 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.21 % Favored : 93.46 % Rotamer: Outliers : 3.02 % Allowed : 19.35 % Favored : 77.63 % 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: 0.55 (0.16), residues: 2736 helix: 1.78 (0.13), residues: 1404 sheet: -0.38 (0.35), residues: 267 loop : -1.42 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 34 TYR 0.013 0.001 TYR E 235 PHE 0.028 0.002 PHE B 357 TRP 0.008 0.001 TRP A 176 HIS 0.006 0.001 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.00319 (21114) covalent geometry : angle 0.50561 (28584) hydrogen bonds : bond 0.04113 ( 1153) hydrogen bonds : angle 4.39834 ( 3390) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7318 (ttm-80) cc_final: 0.6962 (ttp-110) REVERT: A 343 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6628 (tt0) REVERT: A 347 MET cc_start: 0.4305 (mmm) cc_final: 0.1687 (tpp) REVERT: A 417 GLN cc_start: 0.7788 (tp40) cc_final: 0.7455 (tp40) REVERT: A 424 LYS cc_start: 0.8053 (tppt) cc_final: 0.7667 (tttt) REVERT: B 70 PHE cc_start: 0.9526 (OUTLIER) cc_final: 0.9145 (t80) REVERT: B 173 ARG cc_start: 0.8387 (mmt90) cc_final: 0.8092 (mmt-90) REVERT: B 208 MET cc_start: 0.7890 (ptm) cc_final: 0.7456 (ptm) REVERT: B 296 ASP cc_start: 0.2409 (OUTLIER) cc_final: 0.1622 (t0) REVERT: B 396 ARG cc_start: 0.8584 (mtp85) cc_final: 0.8221 (mtt180) REVERT: C 7 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6658 (mm-30) REVERT: C 28 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.6292 (mp10) REVERT: C 282 ARG cc_start: 0.3698 (OUTLIER) cc_final: 0.3191 (mpp-170) REVERT: D 199 TYR cc_start: 0.7649 (m-10) cc_final: 0.7240 (m-10) REVERT: D 219 PHE cc_start: 0.5556 (OUTLIER) cc_final: 0.4820 (m-80) REVERT: D 424 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7864 (mmtp) REVERT: F 70 PHE cc_start: 0.9463 (OUTLIER) cc_final: 0.8507 (t80) REVERT: F 105 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7982 (mm) REVERT: F 149 ASP cc_start: 0.8377 (m-30) cc_final: 0.8142 (m-30) REVERT: F 317 LEU cc_start: 0.7469 (tt) cc_final: 0.6943 (tt) REVERT: F 379 ASN cc_start: 0.8045 (p0) cc_final: 0.7761 (p0) REVERT: F 413 LYS cc_start: 0.8324 (ttpp) cc_final: 0.7894 (tptt) REVERT: E 7 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6821 (mm-30) REVERT: E 247 VAL cc_start: 0.5019 (OUTLIER) cc_final: 0.4684 (p) REVERT: E 249 SER cc_start: 0.6455 (m) cc_final: 0.5201 (p) REVERT: E 347 MET cc_start: 0.4669 (tpp) cc_final: 0.3618 (ptp) REVERT: E 396 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8129 (mtt180) outliers start: 63 outliers final: 33 residues processed: 255 average time/residue: 0.1464 time to fit residues: 57.9989 Evaluate side-chains 230 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 70 PHE Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 341 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 234 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 chunk 160 optimal weight: 0.4980 chunk 248 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 171 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS B 28 GLN D 211 HIS E 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.202303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151072 restraints weight = 22238.651| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.40 r_work: 0.3168 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21114 Z= 0.120 Angle : 0.486 7.157 28584 Z= 0.257 Chirality : 0.040 0.141 3108 Planarity : 0.004 0.050 3774 Dihedral : 3.955 51.530 2944 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.25 % Favored : 93.46 % Rotamer: Outliers : 3.30 % Allowed : 19.35 % Favored : 77.35 % 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: 0.72 (0.17), residues: 2736 helix: 1.94 (0.13), residues: 1386 sheet: -0.60 (0.35), residues: 264 loop : -1.20 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.013 0.001 TYR C 235 PHE 0.012 0.002 PHE A 340 TRP 0.008 0.001 TRP D 187 HIS 0.006 0.001 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.00265 (21114) covalent geometry : angle 0.48608 (28584) hydrogen bonds : bond 0.03751 ( 1153) hydrogen bonds : angle 4.24543 ( 3390) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 200 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8032 (mm) REVERT: A 193 ARG cc_start: 0.7195 (ttm-80) cc_final: 0.6758 (ttp-110) REVERT: A 283 LYS cc_start: 0.5067 (OUTLIER) cc_final: 0.4339 (mttm) REVERT: A 343 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6547 (tt0) REVERT: A 347 MET cc_start: 0.4130 (mmm) cc_final: 0.1589 (tpp) REVERT: A 417 GLN cc_start: 0.7736 (tp40) cc_final: 0.7493 (tp40) REVERT: A 424 LYS cc_start: 0.8045 (tppt) cc_final: 0.7763 (tttt) REVERT: B 28 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.5862 (pm20) REVERT: B 70 PHE cc_start: 0.9476 (OUTLIER) cc_final: 0.9116 (t80) REVERT: B 105 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7897 (mm) REVERT: B 208 MET cc_start: 0.7649 (ptm) cc_final: 0.7222 (ptm) REVERT: C 7 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6531 (mm-30) REVERT: C 70 PHE cc_start: 0.9444 (OUTLIER) cc_final: 0.8446 (t80) REVERT: C 282 ARG cc_start: 0.4117 (OUTLIER) cc_final: 0.3623 (mpp-170) REVERT: D 105 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7789 (mm) REVERT: D 199 TYR cc_start: 0.7992 (m-10) cc_final: 0.7726 (m-10) REVERT: D 219 PHE cc_start: 0.5753 (OUTLIER) cc_final: 0.5172 (m-80) REVERT: F 70 PHE cc_start: 0.9406 (OUTLIER) cc_final: 0.8512 (t80) REVERT: F 105 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7902 (mm) REVERT: F 317 LEU cc_start: 0.7877 (tt) cc_final: 0.7626 (tt) REVERT: F 379 ASN cc_start: 0.8185 (p0) cc_final: 0.7830 (p0) REVERT: F 412 MET cc_start: 0.8408 (mmm) cc_final: 0.8097 (mmm) REVERT: F 413 LYS cc_start: 0.8414 (ttpp) cc_final: 0.8107 (tptt) REVERT: E 7 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7416 (mm-30) REVERT: E 249 SER cc_start: 0.6543 (m) cc_final: 0.5354 (p) REVERT: E 347 MET cc_start: 0.4198 (tpp) cc_final: 0.3791 (ptp) REVERT: E 396 ARG cc_start: 0.8391 (mtp85) cc_final: 0.7956 (mtt180) outliers start: 69 outliers final: 36 residues processed: 261 average time/residue: 0.1555 time to fit residues: 63.9667 Evaluate side-chains 236 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 187 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 70 PHE Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 28 GLN Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 341 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 231 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 212 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 117 optimal weight: 0.0670 chunk 44 optimal weight: 0.8980 chunk 172 optimal weight: 10.0000 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN D 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.199548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.172696 restraints weight = 22353.631| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.15 r_work: 0.3420 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21114 Z= 0.112 Angle : 0.476 7.168 28584 Z= 0.252 Chirality : 0.039 0.140 3108 Planarity : 0.004 0.051 3774 Dihedral : 3.854 51.289 2944 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.14 % Favored : 93.57 % Rotamer: Outliers : 3.16 % Allowed : 19.78 % Favored : 77.06 % 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: 0.82 (0.16), residues: 2736 helix: 2.02 (0.14), residues: 1386 sheet: -0.43 (0.35), residues: 255 loop : -1.20 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.013 0.001 TYR C 235 PHE 0.013 0.002 PHE A 340 TRP 0.006 0.001 TRP F 187 HIS 0.007 0.001 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.00247 (21114) covalent geometry : angle 0.47618 (28584) hydrogen bonds : bond 0.03582 ( 1153) hydrogen bonds : angle 4.15116 ( 3390) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8044 (mm) REVERT: A 193 ARG cc_start: 0.7305 (ttm-80) cc_final: 0.6861 (ttp-110) REVERT: A 208 MET cc_start: 0.7425 (ptm) cc_final: 0.7183 (ptp) REVERT: A 347 MET cc_start: 0.4116 (mmm) cc_final: 0.1581 (tpp) REVERT: A 417 GLN cc_start: 0.7775 (tp40) cc_final: 0.7544 (tp40) REVERT: A 424 LYS cc_start: 0.8039 (tppt) cc_final: 0.7783 (tttt) REVERT: B 28 GLN cc_start: 0.6865 (pp30) cc_final: 0.6542 (pt0) REVERT: B 70 PHE cc_start: 0.9473 (OUTLIER) cc_final: 0.9113 (t80) REVERT: B 105 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7973 (mm) REVERT: B 139 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7054 (mm-30) REVERT: B 208 MET cc_start: 0.7800 (ptm) cc_final: 0.7371 (ptm) REVERT: B 396 ARG cc_start: 0.8574 (mtp85) cc_final: 0.8240 (mtt180) REVERT: C 7 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6686 (mm-30) REVERT: C 70 PHE cc_start: 0.9434 (OUTLIER) cc_final: 0.8432 (t80) REVERT: C 282 ARG cc_start: 0.4371 (OUTLIER) cc_final: 0.3859 (mpp-170) REVERT: D 187 TRP cc_start: 0.9285 (OUTLIER) cc_final: 0.8621 (p-90) REVERT: F 70 PHE cc_start: 0.9396 (OUTLIER) cc_final: 0.8500 (t80) REVERT: F 105 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7916 (mm) REVERT: F 139 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7261 (mm-30) REVERT: F 317 LEU cc_start: 0.7849 (tt) cc_final: 0.7573 (tt) REVERT: F 379 ASN cc_start: 0.8171 (p0) cc_final: 0.7815 (p0) REVERT: F 412 MET cc_start: 0.8439 (mmm) cc_final: 0.8092 (mmm) REVERT: F 424 LYS cc_start: 0.8306 (mmmt) cc_final: 0.7762 (mmtp) REVERT: E 7 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7435 (mm-30) REVERT: E 249 SER cc_start: 0.6676 (m) cc_final: 0.5559 (p) REVERT: E 347 MET cc_start: 0.4259 (tpp) cc_final: 0.3924 (ptp) REVERT: E 396 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8080 (mtt180) outliers start: 66 outliers final: 42 residues processed: 253 average time/residue: 0.1522 time to fit residues: 60.9502 Evaluate side-chains 241 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 70 PHE Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 341 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 80 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 31 optimal weight: 30.0000 chunk 216 optimal weight: 30.0000 chunk 50 optimal weight: 0.2980 chunk 147 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN D 211 HIS E 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.200840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3611 r_free = 0.3611 target = 0.145693 restraints weight = 22262.828| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.53 r_work: 0.3107 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21114 Z= 0.156 Angle : 0.510 6.818 28584 Z= 0.269 Chirality : 0.040 0.136 3108 Planarity : 0.004 0.050 3774 Dihedral : 4.013 59.757 2944 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.58 % Favored : 93.09 % Rotamer: Outliers : 3.69 % Allowed : 19.64 % Favored : 76.68 % 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: 0.70 (0.16), residues: 2736 helix: 1.93 (0.13), residues: 1386 sheet: -0.75 (0.34), residues: 264 loop : -1.18 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 407 TYR 0.011 0.001 TYR C 235 PHE 0.019 0.002 PHE D 219 TRP 0.006 0.001 TRP A 176 HIS 0.010 0.001 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.00361 (21114) covalent geometry : angle 0.51035 (28584) hydrogen bonds : bond 0.04155 ( 1153) hydrogen bonds : angle 4.23478 ( 3390) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 197 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8005 (mm) REVERT: A 283 LYS cc_start: 0.5001 (OUTLIER) cc_final: 0.4386 (mttm) REVERT: A 347 MET cc_start: 0.4307 (mmm) cc_final: 0.2257 (tpp) REVERT: A 417 GLN cc_start: 0.7773 (tp40) cc_final: 0.7477 (tp40) REVERT: A 424 LYS cc_start: 0.8090 (tppt) cc_final: 0.7792 (tttt) REVERT: B 28 GLN cc_start: 0.6742 (pp30) cc_final: 0.6364 (pm20) REVERT: B 70 PHE cc_start: 0.9510 (OUTLIER) cc_final: 0.9134 (t80) REVERT: B 219 PHE cc_start: 0.5944 (OUTLIER) cc_final: 0.5676 (m-80) REVERT: C 7 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6484 (mm-30) REVERT: C 70 PHE cc_start: 0.9498 (OUTLIER) cc_final: 0.8442 (t80) REVERT: C 149 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7645 (t0) REVERT: C 282 ARG cc_start: 0.4414 (OUTLIER) cc_final: 0.3884 (mpp-170) REVERT: D 105 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7800 (mm) REVERT: D 187 TRP cc_start: 0.9279 (OUTLIER) cc_final: 0.8588 (p-90) REVERT: D 424 LYS cc_start: 0.8288 (mtpt) cc_final: 0.8001 (mmtp) REVERT: F 70 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.8491 (t80) REVERT: F 317 LEU cc_start: 0.7770 (tt) cc_final: 0.7430 (tt) REVERT: F 379 ASN cc_start: 0.8080 (p0) cc_final: 0.7570 (p0) REVERT: F 412 MET cc_start: 0.8372 (mmm) cc_final: 0.7998 (mmm) REVERT: F 424 LYS cc_start: 0.8352 (mmmt) cc_final: 0.7806 (mmtp) REVERT: E 7 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: E 249 SER cc_start: 0.6544 (m) cc_final: 0.5294 (p) REVERT: E 347 MET cc_start: 0.4305 (tpp) cc_final: 0.4047 (ptp) REVERT: E 396 ARG cc_start: 0.8434 (mtp85) cc_final: 0.7975 (mtt180) outliers start: 77 outliers final: 53 residues processed: 259 average time/residue: 0.1550 time to fit residues: 63.8273 Evaluate side-chains 253 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 70 PHE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 28 GLN Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 341 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 207 optimal weight: 5.9990 chunk 194 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 248 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 236 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN D 211 HIS E 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.202114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.161243 restraints weight = 22182.459| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.51 r_work: 0.3244 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21114 Z= 0.115 Angle : 0.476 7.093 28584 Z= 0.251 Chirality : 0.039 0.134 3108 Planarity : 0.004 0.050 3774 Dihedral : 3.879 58.662 2944 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.32 % Favored : 93.42 % Rotamer: Outliers : 3.54 % Allowed : 19.88 % Favored : 76.58 % 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: 0.80 (0.16), residues: 2736 helix: 2.02 (0.14), residues: 1386 sheet: -0.55 (0.35), residues: 255 loop : -1.20 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.012 0.001 TYR C 235 PHE 0.016 0.002 PHE D 219 TRP 0.005 0.001 TRP E 187 HIS 0.011 0.001 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.00254 (21114) covalent geometry : angle 0.47560 (28584) hydrogen bonds : bond 0.03667 ( 1153) hydrogen bonds : angle 4.11177 ( 3390) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 199 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8053 (mm) REVERT: A 283 LYS cc_start: 0.5047 (OUTLIER) cc_final: 0.4157 (mttm) REVERT: A 347 MET cc_start: 0.4130 (mmm) cc_final: 0.2179 (tpp) REVERT: B 28 GLN cc_start: 0.6699 (OUTLIER) cc_final: 0.6317 (pm20) REVERT: B 70 PHE cc_start: 0.9477 (OUTLIER) cc_final: 0.9112 (t80) REVERT: B 105 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7887 (mm) REVERT: B 139 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6842 (mm-30) REVERT: B 206 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: B 208 MET cc_start: 0.7381 (ptm) cc_final: 0.7139 (ptm) REVERT: B 396 ARG cc_start: 0.8541 (mtp85) cc_final: 0.8221 (mtt180) REVERT: C 7 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6698 (mm-30) REVERT: C 70 PHE cc_start: 0.9449 (OUTLIER) cc_final: 0.8406 (t80) REVERT: C 149 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7605 (t0) REVERT: C 282 ARG cc_start: 0.4602 (OUTLIER) cc_final: 0.4185 (mpp-170) REVERT: D 105 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7878 (mm) REVERT: D 187 TRP cc_start: 0.9272 (OUTLIER) cc_final: 0.8653 (p-90) REVERT: F 70 PHE cc_start: 0.9406 (OUTLIER) cc_final: 0.8464 (t80) REVERT: F 105 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7882 (mm) REVERT: F 139 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7209 (mm-30) REVERT: F 317 LEU cc_start: 0.8027 (tt) cc_final: 0.7752 (tt) REVERT: F 379 ASN cc_start: 0.8106 (p0) cc_final: 0.7711 (p0) REVERT: F 412 MET cc_start: 0.8431 (mmm) cc_final: 0.8053 (mmm) REVERT: F 424 LYS cc_start: 0.8249 (mmmt) cc_final: 0.7755 (mmtp) REVERT: E 7 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7467 (mm-30) REVERT: E 249 SER cc_start: 0.6606 (m) cc_final: 0.5587 (p) outliers start: 74 outliers final: 50 residues processed: 261 average time/residue: 0.1543 time to fit residues: 63.8364 Evaluate side-chains 255 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 70 PHE Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 28 GLN Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 341 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 200 optimal weight: 7.9990 chunk 79 optimal weight: 30.0000 chunk 123 optimal weight: 6.9990 chunk 253 optimal weight: 0.5980 chunk 236 optimal weight: 0.7980 chunk 268 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 HIS E 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.200407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.152934 restraints weight = 22145.883| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.40 r_work: 0.3183 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21114 Z= 0.158 Angle : 0.511 6.788 28584 Z= 0.269 Chirality : 0.041 0.169 3108 Planarity : 0.004 0.051 3774 Dihedral : 3.995 59.058 2944 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.65 % Favored : 93.09 % Rotamer: Outliers : 3.50 % Allowed : 19.73 % Favored : 76.77 % 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: 0.64 (0.16), residues: 2736 helix: 1.92 (0.13), residues: 1386 sheet: -0.99 (0.32), residues: 288 loop : -1.21 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 407 TYR 0.010 0.001 TYR C 235 PHE 0.020 0.002 PHE D 219 TRP 0.007 0.001 TRP A 176 HIS 0.008 0.001 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.00367 (21114) covalent geometry : angle 0.51141 (28584) hydrogen bonds : bond 0.04151 ( 1153) hydrogen bonds : angle 4.19332 ( 3390) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 188 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8070 (mm) REVERT: A 150 VAL cc_start: 0.8421 (t) cc_final: 0.8200 (t) REVERT: A 283 LYS cc_start: 0.5187 (OUTLIER) cc_final: 0.4364 (mttm) REVERT: A 347 MET cc_start: 0.4334 (mmm) cc_final: 0.2306 (tpp) REVERT: B 28 GLN cc_start: 0.6801 (pp30) cc_final: 0.6332 (pt0) REVERT: B 70 PHE cc_start: 0.9506 (OUTLIER) cc_final: 0.9126 (t80) REVERT: B 105 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7893 (mm) REVERT: B 206 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: B 208 MET cc_start: 0.7503 (ptm) cc_final: 0.7222 (ptm) REVERT: B 396 ARG cc_start: 0.8553 (mtp85) cc_final: 0.8169 (mtt180) REVERT: C 7 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6577 (mm-30) REVERT: C 70 PHE cc_start: 0.9481 (OUTLIER) cc_final: 0.8464 (t80) REVERT: C 149 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7659 (t0) REVERT: C 282 ARG cc_start: 0.4512 (OUTLIER) cc_final: 0.4118 (mpp-170) REVERT: D 105 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7813 (mm) REVERT: D 187 TRP cc_start: 0.9266 (OUTLIER) cc_final: 0.8658 (p-90) REVERT: F 70 PHE cc_start: 0.9455 (OUTLIER) cc_final: 0.8462 (t80) REVERT: F 105 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7900 (mm) REVERT: F 139 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7103 (mm-30) REVERT: F 317 LEU cc_start: 0.7976 (tt) cc_final: 0.7457 (tt) REVERT: F 343 GLU cc_start: 0.8082 (tp30) cc_final: 0.7772 (tp30) REVERT: F 379 ASN cc_start: 0.8082 (p0) cc_final: 0.7504 (p0) REVERT: F 412 MET cc_start: 0.8377 (mmm) cc_final: 0.7958 (mmm) REVERT: F 424 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7713 (mmtp) REVERT: E 7 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7267 (mm-30) REVERT: E 249 SER cc_start: 0.6705 (m) cc_final: 0.5528 (p) REVERT: E 396 ARG cc_start: 0.8436 (mtp85) cc_final: 0.7948 (mtt180) outliers start: 73 outliers final: 51 residues processed: 250 average time/residue: 0.1503 time to fit residues: 60.0391 Evaluate side-chains 247 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 182 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 70 PHE Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 371 TRP Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 28 GLN Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 341 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 146 optimal weight: 0.5980 chunk 217 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 chunk 246 optimal weight: 30.0000 chunk 161 optimal weight: 7.9990 chunk 143 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 211 optimal weight: 0.9990 chunk 114 optimal weight: 30.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 HIS E 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.196779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152382 restraints weight = 21968.369| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.42 r_work: 0.3145 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21114 Z= 0.171 Angle : 0.522 6.686 28584 Z= 0.275 Chirality : 0.041 0.139 3108 Planarity : 0.004 0.059 3774 Dihedral : 4.064 58.249 2944 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.80 % Favored : 92.95 % Rotamer: Outliers : 3.69 % Allowed : 19.97 % Favored : 76.34 % 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: 0.56 (0.16), residues: 2736 helix: 1.86 (0.13), residues: 1386 sheet: -1.06 (0.32), residues: 288 loop : -1.24 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 407 TYR 0.010 0.001 TYR B 77 PHE 0.022 0.002 PHE D 219 TRP 0.007 0.001 TRP C 187 HIS 0.010 0.001 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.00399 (21114) covalent geometry : angle 0.52172 (28584) hydrogen bonds : bond 0.04313 ( 1153) hydrogen bonds : angle 4.23997 ( 3390) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 187 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8036 (mm) REVERT: A 150 VAL cc_start: 0.8545 (t) cc_final: 0.8320 (t) REVERT: A 283 LYS cc_start: 0.5367 (OUTLIER) cc_final: 0.4600 (mttm) REVERT: A 347 MET cc_start: 0.4422 (mmm) cc_final: 0.2489 (tpp) REVERT: B 28 GLN cc_start: 0.6760 (pp30) cc_final: 0.6277 (pt0) REVERT: B 70 PHE cc_start: 0.9556 (OUTLIER) cc_final: 0.9192 (t80) REVERT: B 105 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7910 (mm) REVERT: B 206 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: B 208 MET cc_start: 0.7846 (ptm) cc_final: 0.7536 (ptm) REVERT: B 396 ARG cc_start: 0.8624 (mtp85) cc_final: 0.8204 (mtt180) REVERT: C 7 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6714 (mm-30) REVERT: C 70 PHE cc_start: 0.9520 (OUTLIER) cc_final: 0.8495 (t80) REVERT: C 149 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7933 (t0) REVERT: C 226 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6585 (mm) REVERT: C 282 ARG cc_start: 0.4153 (OUTLIER) cc_final: 0.3732 (mpp-170) REVERT: D 173 ARG cc_start: 0.8239 (mmt90) cc_final: 0.7976 (mmt-90) REVERT: D 187 TRP cc_start: 0.9293 (OUTLIER) cc_final: 0.8709 (p-90) REVERT: F 70 PHE cc_start: 0.9496 (OUTLIER) cc_final: 0.8475 (t80) REVERT: F 105 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8014 (mm) REVERT: F 317 LEU cc_start: 0.7908 (tt) cc_final: 0.7375 (tt) REVERT: F 343 GLU cc_start: 0.8301 (tp30) cc_final: 0.7806 (tp30) REVERT: F 412 MET cc_start: 0.8351 (mmm) cc_final: 0.7930 (mmm) REVERT: F 424 LYS cc_start: 0.8366 (mmmt) cc_final: 0.7805 (mmtp) REVERT: E 7 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7487 (mm-30) REVERT: E 249 SER cc_start: 0.6646 (m) cc_final: 0.5428 (p) REVERT: E 396 ARG cc_start: 0.8512 (mtp85) cc_final: 0.8114 (mtt180) outliers start: 77 outliers final: 52 residues processed: 252 average time/residue: 0.1508 time to fit residues: 60.2225 Evaluate side-chains 251 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 185 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 70 PHE Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 28 GLN Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.9788 > 50: distance: 18 - 59: 23.316 distance: 22 - 26: 34.558 distance: 26 - 27: 33.855 distance: 27 - 28: 39.490 distance: 27 - 30: 19.330 distance: 28 - 34: 68.836 distance: 30 - 31: 31.659 distance: 31 - 32: 12.106 distance: 31 - 33: 35.685 distance: 34 - 35: 41.149 distance: 35 - 36: 12.386 distance: 35 - 38: 14.725 distance: 36 - 37: 18.831 distance: 36 - 40: 16.141 distance: 38 - 39: 29.716 distance: 40 - 41: 25.576 distance: 41 - 42: 28.627 distance: 41 - 44: 38.929 distance: 42 - 43: 32.679 distance: 42 - 49: 30.491 distance: 44 - 45: 39.097 distance: 45 - 46: 39.952 distance: 46 - 47: 17.386 distance: 46 - 48: 23.642 distance: 49 - 50: 13.313 distance: 50 - 51: 24.634 distance: 51 - 52: 25.864 distance: 51 - 53: 20.789 distance: 53 - 54: 26.823 distance: 53 - 190: 26.027 distance: 54 - 55: 22.611 distance: 54 - 57: 25.965 distance: 55 - 56: 38.846 distance: 55 - 59: 20.621 distance: 56 - 187: 28.788 distance: 57 - 58: 22.634 distance: 59 - 60: 16.371 distance: 60 - 61: 13.786 distance: 60 - 63: 20.355 distance: 61 - 62: 19.780 distance: 61 - 67: 21.666 distance: 63 - 64: 27.531 distance: 64 - 65: 3.373 distance: 64 - 66: 37.535 distance: 67 - 68: 20.611 distance: 68 - 69: 15.390 distance: 68 - 71: 17.003 distance: 69 - 70: 13.742 distance: 69 - 75: 5.622 distance: 70 - 170: 15.646 distance: 71 - 72: 11.713 distance: 71 - 73: 22.179 distance: 72 - 74: 10.152 distance: 75 - 76: 5.715 distance: 76 - 79: 14.951 distance: 77 - 78: 23.976 distance: 77 - 82: 5.984 distance: 79 - 80: 17.966 distance: 79 - 81: 20.731 distance: 82 - 83: 19.653 distance: 83 - 84: 16.570 distance: 83 - 86: 19.727 distance: 84 - 85: 4.719 distance: 84 - 91: 25.753 distance: 86 - 87: 23.302 distance: 87 - 88: 7.981 distance: 89 - 90: 15.914 distance: 91 - 92: 11.429 distance: 92 - 93: 16.467 distance: 92 - 95: 13.004 distance: 93 - 94: 16.111 distance: 93 - 99: 6.886 distance: 95 - 96: 14.662 distance: 96 - 97: 20.216 distance: 96 - 98: 13.570