Starting phenix.real_space_refine on Wed Jun 18 04:48:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1m_39730/06_2025/8z1m_39730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1m_39730/06_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_39730/06_2025/8z1m_39730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1m_39730/06_2025/8z1m_39730.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1m_39730/06_2025/8z1m_39730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1m_39730/06_2025/8z1m_39730.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.47, per 1000 atoms: 0.60 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: 5.18 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 1.96 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: 6.86 Time building geometry restraints manager: 5.95 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: 0.03 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: 1.700 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: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 45.400 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.080 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (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 TRP 0.096 0.015 TRP A 460 HIS 0.022 0.005 HIS D 143 PHE 0.086 0.009 PHE B 66 TYR 0.063 0.011 TYR D 164 ARG 0.035 0.005 ARG F 142 Details of bonding type rmsd hydrogen bonds : bond 0.13554 ( 1153) hydrogen bonds : angle 5.50738 ( 3390) covalent geometry : bond 0.01133 (21114) covalent geometry : angle 1.08272 (28584) *********************** 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 : 2.156 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: 0.3216 time to fit residues: 115.1127 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 : 2.295 ------------------------------------------------------------------------------- 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 227 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 69 optimal weight: 40.0000 chunk 138 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 360 HIS A 379 ASN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN ** E 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.197999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.145599 restraints weight = 22377.445| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.44 r_work: 0.3111 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 21114 Z= 0.247 Angle : 0.623 8.768 28584 Z= 0.329 Chirality : 0.044 0.145 3108 Planarity : 0.005 0.065 3774 Dihedral : 4.722 64.818 2956 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.16 % Favored : 92.47 % Rotamer: Outliers : 3.30 % Allowed : 19.78 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2736 helix: 1.45 (0.13), residues: 1401 sheet: -0.72 (0.35), residues: 273 loop : -1.56 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 176 HIS 0.004 0.001 HIS A 207 PHE 0.018 0.003 PHE D 119 TYR 0.017 0.002 TYR F 235 ARG 0.005 0.001 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.05293 ( 1153) hydrogen bonds : angle 4.79188 ( 3390) covalent geometry : bond 0.00581 (21114) covalent geometry : angle 0.62303 (28584) *********************** 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 268 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 199 time to evaluate : 2.207 Fit side-chains revert: symmetry clash REVERT: A 174 ASN cc_start: 0.7654 (p0) cc_final: 0.7440 (p0) REVERT: A 308 VAL cc_start: 0.2011 (OUTLIER) cc_final: 0.1810 (t) REVERT: A 343 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6524 (tt0) REVERT: B 28 GLN cc_start: 0.6465 (pp30) cc_final: 0.6167 (pt0) REVERT: B 70 PHE cc_start: 0.9540 (OUTLIER) cc_final: 0.9162 (t80) REVERT: B 208 MET cc_start: 0.7670 (ptm) cc_final: 0.7379 (ptm) REVERT: B 296 ASP cc_start: 0.2422 (OUTLIER) cc_final: 0.1692 (t0) REVERT: B 396 ARG cc_start: 0.8520 (mtp85) cc_final: 0.8115 (mtt180) REVERT: C 7 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6551 (mm-30) REVERT: C 246 ARG cc_start: 0.4919 (OUTLIER) cc_final: 0.4715 (tpp-160) REVERT: C 282 ARG cc_start: 0.4185 (OUTLIER) cc_final: 0.3602 (mpp-170) REVERT: D 219 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5453 (m-80) REVERT: D 254 GLN cc_start: 0.4659 (OUTLIER) cc_final: 0.3702 (mp10) REVERT: F 438 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7448 (t) REVERT: E 70 PHE cc_start: 0.9496 (OUTLIER) cc_final: 0.9173 (t80) REVERT: E 347 MET cc_start: 0.4759 (tpp) cc_final: 0.3371 (mtm) REVERT: E 396 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8053 (mtt180) REVERT: E 402 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6825 (pm20) outliers start: 69 outliers final: 35 residues processed: 260 average time/residue: 0.3524 time to fit residues: 140.9501 Evaluate side-chains 225 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 2.126 ------------------------------------------------------------------------------- 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 308 VAL 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 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 296 ASP Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 341 ILE 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 219 PHE Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 254 GLN Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 383 VAL 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 315 VAL Chi-restraints excluded: chain F residue 415 CYS 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 70 PHE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 248 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 Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 211 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 246 optimal weight: 20.0000 chunk 204 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.197193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.146683 restraints weight = 22303.704| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.41 r_work: 0.3097 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 21114 Z= 0.253 Angle : 0.608 6.894 28584 Z= 0.322 Chirality : 0.044 0.172 3108 Planarity : 0.005 0.052 3774 Dihedral : 4.485 46.063 2942 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.20 % Favored : 92.43 % Rotamer: Outliers : 4.07 % Allowed : 20.59 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2736 helix: 1.42 (0.13), residues: 1383 sheet: -0.78 (0.34), residues: 267 loop : -1.49 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 176 HIS 0.006 0.001 HIS D 211 PHE 0.027 0.003 PHE B 357 TYR 0.013 0.002 TYR B 372 ARG 0.006 0.001 ARG B 361 Details of bonding type rmsd hydrogen bonds : bond 0.05362 ( 1153) hydrogen bonds : angle 4.72143 ( 3390) covalent geometry : bond 0.00597 (21114) covalent geometry : angle 0.60821 (28584) *********************** 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 272 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 187 time to evaluate : 2.024 Fit side-chains revert: symmetry clash REVERT: A 24 SER cc_start: 0.8011 (t) cc_final: 0.7703 (p) REVERT: A 70 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.9093 (t80) REVERT: A 343 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6646 (tt0) REVERT: A 424 LYS cc_start: 0.8024 (tppt) cc_final: 0.7757 (tttp) REVERT: B 28 GLN cc_start: 0.6670 (pp30) cc_final: 0.6190 (pt0) REVERT: B 29 LYS cc_start: 0.6890 (mtpt) cc_final: 0.6653 (tttt) REVERT: B 70 PHE cc_start: 0.9538 (OUTLIER) cc_final: 0.9168 (t80) REVERT: B 206 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: B 208 MET cc_start: 0.7702 (ptm) cc_final: 0.7381 (ptm) REVERT: B 296 ASP cc_start: 0.2461 (OUTLIER) cc_final: 0.1666 (t0) REVERT: C 7 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6606 (mm-30) REVERT: C 70 PHE cc_start: 0.9525 (OUTLIER) cc_final: 0.8478 (t80) REVERT: C 149 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7608 (t0) REVERT: C 282 ARG cc_start: 0.4244 (OUTLIER) cc_final: 0.3759 (mpp-170) REVERT: D 187 TRP cc_start: 0.9277 (OUTLIER) cc_final: 0.8680 (p-90) REVERT: D 424 LYS cc_start: 0.8319 (mtpt) cc_final: 0.8040 (mmtp) REVERT: F 70 PHE cc_start: 0.9470 (OUTLIER) cc_final: 0.8418 (t80) REVERT: F 438 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7611 (t) REVERT: E 7 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7332 (mm-30) REVERT: E 70 PHE cc_start: 0.9495 (OUTLIER) cc_final: 0.9189 (t80) REVERT: E 249 SER cc_start: 0.6574 (m) cc_final: 0.5380 (p) REVERT: E 347 MET cc_start: 0.4577 (tpp) cc_final: 0.3620 (ptp) REVERT: E 396 ARG cc_start: 0.8483 (mtp85) cc_final: 0.8053 (mtt180) REVERT: E 402 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6866 (pm20) outliers start: 85 outliers final: 47 residues processed: 263 average time/residue: 0.3196 time to fit residues: 133.4474 Evaluate side-chains 236 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 2.128 ------------------------------------------------------------------------------- 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 149 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 THR 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 141 CYS Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 248 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 321 THR Chi-restraints excluded: chain B residue 354 ILE 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 62 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 24 SER 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 219 PHE Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 383 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 78 LYS 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 70 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 174 ASN 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 248 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 162 optimal weight: 7.9990 chunk 152 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 262 optimal weight: 0.8980 chunk 22 optimal weight: 20.0000 chunk 154 optimal weight: 0.0050 chunk 10 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 220 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 HIS F 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.203081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.152611 restraints weight = 22420.493| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.45 r_work: 0.3166 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21114 Z= 0.103 Angle : 0.477 7.787 28584 Z= 0.254 Chirality : 0.039 0.130 3108 Planarity : 0.004 0.052 3774 Dihedral : 3.878 30.344 2942 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.85 % Favored : 93.79 % Rotamer: Outliers : 3.07 % Allowed : 21.22 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2736 helix: 1.85 (0.14), residues: 1386 sheet: -0.64 (0.35), residues: 255 loop : -1.32 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 187 HIS 0.009 0.001 HIS D 211 PHE 0.019 0.002 PHE C 219 TYR 0.011 0.001 TYR E 235 ARG 0.004 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 1153) hydrogen bonds : angle 4.24470 ( 3390) covalent geometry : bond 0.00218 (21114) covalent geometry : angle 0.47729 (28584) *********************** 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 271 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 207 time to evaluate : 2.327 Fit side-chains revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7871 (mm) REVERT: A 193 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.7003 (ttm-80) REVERT: A 343 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6580 (tt0) REVERT: A 347 MET cc_start: 0.4379 (mmm) cc_final: 0.1710 (tpp) REVERT: A 417 GLN cc_start: 0.7760 (tp40) cc_final: 0.7496 (tp40) REVERT: A 424 LYS cc_start: 0.7964 (tppt) cc_final: 0.7719 (tttp) REVERT: B 70 PHE cc_start: 0.9467 (OUTLIER) cc_final: 0.9182 (t80) REVERT: B 105 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7710 (mm) REVERT: B 199 TYR cc_start: 0.8100 (m-10) cc_final: 0.7864 (m-10) REVERT: B 208 MET cc_start: 0.7636 (ptm) cc_final: 0.7246 (ptm) REVERT: B 296 ASP cc_start: 0.2401 (OUTLIER) cc_final: 0.1561 (t0) REVERT: B 396 ARG cc_start: 0.8492 (mtp85) cc_final: 0.8069 (mtt180) REVERT: C 7 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6596 (mm-30) REVERT: C 70 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.8422 (t80) REVERT: C 206 GLU cc_start: 0.7253 (mm-30) cc_final: 0.7035 (mm-30) REVERT: C 282 ARG cc_start: 0.4172 (OUTLIER) cc_final: 0.3594 (mpp-170) REVERT: D 187 TRP cc_start: 0.9285 (OUTLIER) cc_final: 0.8623 (p-90) REVERT: D 424 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8021 (mmtp) REVERT: F 70 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.8525 (t80) REVERT: F 105 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7682 (mm) REVERT: F 317 LEU cc_start: 0.8025 (tt) cc_final: 0.7670 (tt) REVERT: F 424 LYS cc_start: 0.8319 (mmmt) cc_final: 0.7755 (mmtp) REVERT: E 7 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6636 (mm-30) REVERT: E 175 SER cc_start: 0.8969 (OUTLIER) cc_final: 0.8747 (p) REVERT: E 249 SER cc_start: 0.6766 (m) cc_final: 0.5529 (p) REVERT: E 347 MET cc_start: 0.4436 (tpp) cc_final: 0.3947 (ptp) outliers start: 64 outliers final: 27 residues processed: 262 average time/residue: 0.3199 time to fit residues: 132.1779 Evaluate side-chains 228 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 2.124 ------------------------------------------------------------------------------- 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 149 ASP Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 70 PHE 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 187 TRP Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain F residue 26 LEU 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 379 ASN Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 27 PHE 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 341 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 53 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 246 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN D 211 HIS ** E 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.198311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.153968 restraints weight = 22366.609| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.55 r_work: 0.3148 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 21114 Z= 0.210 Angle : 0.563 6.689 28584 Z= 0.296 Chirality : 0.042 0.150 3108 Planarity : 0.005 0.050 3774 Dihedral : 4.174 22.376 2942 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.27 % Favored : 92.36 % Rotamer: Outliers : 3.83 % Allowed : 21.12 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2736 helix: 1.66 (0.13), residues: 1386 sheet: -1.02 (0.33), residues: 282 loop : -1.26 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 176 HIS 0.007 0.001 HIS D 211 PHE 0.016 0.002 PHE C 219 TYR 0.012 0.001 TYR B 77 ARG 0.005 0.001 ARG B 361 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 1153) hydrogen bonds : angle 4.46071 ( 3390) covalent geometry : bond 0.00492 (21114) covalent geometry : angle 0.56311 (28584) *********************** 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 271 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 191 time to evaluate : 2.204 Fit side-chains revert: symmetry clash REVERT: A 150 VAL cc_start: 0.8581 (t) cc_final: 0.8259 (t) REVERT: A 219 PHE cc_start: 0.4870 (OUTLIER) cc_final: 0.4515 (m-80) REVERT: A 283 LYS cc_start: 0.5297 (OUTLIER) cc_final: 0.4656 (mttm) REVERT: B 70 PHE cc_start: 0.9532 (OUTLIER) cc_final: 0.9143 (t80) REVERT: B 206 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: B 219 PHE cc_start: 0.6208 (OUTLIER) cc_final: 0.5885 (m-80) REVERT: C 7 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6621 (mm-30) REVERT: C 70 PHE cc_start: 0.9523 (OUTLIER) cc_final: 0.8432 (t80) REVERT: C 149 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7758 (t0) REVERT: C 219 PHE cc_start: 0.6311 (OUTLIER) cc_final: 0.5751 (m-80) REVERT: C 282 ARG cc_start: 0.4566 (OUTLIER) cc_final: 0.4136 (mpp-170) REVERT: C 370 ILE cc_start: 0.3713 (OUTLIER) cc_final: 0.3513 (tt) REVERT: D 187 TRP cc_start: 0.9264 (OUTLIER) cc_final: 0.8730 (p-90) REVERT: D 424 LYS cc_start: 0.8273 (mtpt) cc_final: 0.8031 (mmtp) REVERT: F 70 PHE cc_start: 0.9501 (OUTLIER) cc_final: 0.8445 (t80) REVERT: F 317 LEU cc_start: 0.8045 (tt) cc_final: 0.7767 (tt) REVERT: F 424 LYS cc_start: 0.8346 (mmmt) cc_final: 0.7807 (mmtp) REVERT: F 438 VAL cc_start: 0.7808 (OUTLIER) cc_final: 0.7492 (t) REVERT: E 7 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: E 249 SER cc_start: 0.6503 (m) cc_final: 0.5415 (p) REVERT: E 347 MET cc_start: 0.4099 (tpp) cc_final: 0.3887 (ptp) REVERT: E 402 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6690 (pm20) outliers start: 80 outliers final: 47 residues processed: 261 average time/residue: 0.3141 time to fit residues: 129.9448 Evaluate side-chains 244 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 181 time to evaluate : 2.012 ------------------------------------------------------------------------------- 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 141 CYS Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 219 PHE 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 141 CYS Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 180 LEU 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 296 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 321 THR 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 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 341 ILE Chi-restraints excluded: chain C residue 370 ILE 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 141 CYS Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 341 ILE 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 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 26 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 106 THR 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 341 ILE Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 55 optimal weight: 0.0060 chunk 204 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 34 optimal weight: 0.4980 chunk 184 optimal weight: 0.6980 chunk 237 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 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 = 0.4196 r_free = 0.4196 target = 0.201975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.150817 restraints weight = 22312.913| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.42 r_work: 0.3158 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2311 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= 0.109 Angle : 0.481 7.412 28584 Z= 0.254 Chirality : 0.039 0.137 3108 Planarity : 0.004 0.052 3774 Dihedral : 3.817 21.133 2942 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.18 % Favored : 93.53 % Rotamer: Outliers : 3.16 % Allowed : 21.98 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.16), residues: 2736 helix: 1.91 (0.14), residues: 1386 sheet: -0.63 (0.35), residues: 255 loop : -1.23 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 187 HIS 0.008 0.001 HIS D 211 PHE 0.018 0.002 PHE C 219 TYR 0.010 0.001 TYR E 235 ARG 0.003 0.000 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 1153) hydrogen bonds : angle 4.17632 ( 3390) covalent geometry : bond 0.00239 (21114) covalent geometry : angle 0.48073 (28584) *********************** 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 263 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 2.207 Fit side-chains REVERT: A 105 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7877 (mm) REVERT: A 283 LYS cc_start: 0.5370 (OUTLIER) cc_final: 0.4692 (mttm) REVERT: A 347 MET cc_start: 0.4189 (mmm) cc_final: 0.2291 (tpp) REVERT: B 70 PHE cc_start: 0.9510 (OUTLIER) cc_final: 0.9198 (t80) REVERT: B 219 PHE cc_start: 0.5915 (OUTLIER) cc_final: 0.5681 (m-80) REVERT: B 396 ARG cc_start: 0.8511 (mtp85) cc_final: 0.8035 (mtt180) REVERT: C 7 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6567 (mm-30) REVERT: C 70 PHE cc_start: 0.9464 (OUTLIER) cc_final: 0.8492 (t80) REVERT: C 206 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6269 (mm-30) REVERT: C 219 PHE cc_start: 0.6137 (OUTLIER) cc_final: 0.5481 (m-80) REVERT: C 282 ARG cc_start: 0.4428 (OUTLIER) cc_final: 0.3968 (mpp-170) REVERT: D 105 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7763 (mm) REVERT: D 187 TRP cc_start: 0.9268 (OUTLIER) cc_final: 0.8695 (p-90) REVERT: D 424 LYS cc_start: 0.8330 (mtpt) cc_final: 0.8026 (mmtp) REVERT: F 70 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.8464 (t80) REVERT: F 317 LEU cc_start: 0.7766 (tt) cc_final: 0.7406 (tt) REVERT: F 402 GLU cc_start: 0.7082 (mp0) cc_final: 0.6681 (mm-30) REVERT: F 424 LYS cc_start: 0.8359 (mmmt) cc_final: 0.7784 (mmtp) REVERT: E 7 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6665 (mm-30) REVERT: E 249 SER cc_start: 0.6621 (m) cc_final: 0.5411 (p) REVERT: E 402 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6548 (pm20) outliers start: 66 outliers final: 40 residues processed: 257 average time/residue: 0.3117 time to fit residues: 126.3519 Evaluate side-chains 246 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 2.040 ------------------------------------------------------------------------------- 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 283 LYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 224 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 321 THR 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 29 LYS 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 187 TRP Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 334 ILE 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 315 VAL Chi-restraints excluded: chain F residue 379 ASN 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 27 PHE Chi-restraints excluded: chain E residue 28 GLN 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 Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 38 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 50 optimal weight: 0.0050 chunk 198 optimal weight: 8.9990 chunk 247 optimal weight: 0.0050 chunk 17 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 overall best weight: 0.5610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4168 r_free = 0.4168 target = 0.200223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.155222 restraints weight = 21997.620| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.39 r_work: 0.3203 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21114 Z= 0.099 Angle : 0.466 7.451 28584 Z= 0.245 Chirality : 0.039 0.192 3108 Planarity : 0.004 0.054 3774 Dihedral : 3.687 19.951 2942 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.07 % Favored : 93.64 % Rotamer: Outliers : 3.30 % Allowed : 21.70 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.16), residues: 2736 helix: 2.04 (0.14), residues: 1386 sheet: -0.47 (0.35), residues: 255 loop : -1.18 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 187 HIS 0.009 0.001 HIS D 211 PHE 0.016 0.001 PHE E 27 TYR 0.010 0.001 TYR E 235 ARG 0.002 0.000 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 1153) hydrogen bonds : angle 4.04728 ( 3390) covalent geometry : bond 0.00213 (21114) covalent geometry : angle 0.46561 (28584) *********************** 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 270 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 201 time to evaluate : 2.075 Fit side-chains REVERT: A 187 TRP cc_start: 0.9244 (OUTLIER) cc_final: 0.8601 (p-90) REVERT: A 283 LYS cc_start: 0.5386 (OUTLIER) cc_final: 0.4751 (mttm) REVERT: A 347 MET cc_start: 0.4298 (mmm) cc_final: 0.2520 (tpp) REVERT: A 417 GLN cc_start: 0.7826 (tp40) cc_final: 0.7535 (tp40) REVERT: B 70 PHE cc_start: 0.9509 (OUTLIER) cc_final: 0.9209 (t80) REVERT: B 105 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7977 (mm) REVERT: B 206 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: B 219 PHE cc_start: 0.5732 (OUTLIER) cc_final: 0.5493 (m-80) REVERT: C 7 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6696 (mm-30) REVERT: C 70 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.8453 (t80) REVERT: C 206 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6389 (mm-30) REVERT: C 219 PHE cc_start: 0.5971 (OUTLIER) cc_final: 0.5255 (m-80) REVERT: C 226 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6630 (mm) REVERT: C 282 ARG cc_start: 0.4271 (OUTLIER) cc_final: 0.3791 (mpp-170) REVERT: D 105 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7856 (mm) REVERT: D 187 TRP cc_start: 0.9284 (OUTLIER) cc_final: 0.8640 (p-90) REVERT: D 206 GLU cc_start: 0.7247 (mm-30) cc_final: 0.7008 (mm-30) REVERT: D 424 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7963 (mmtp) REVERT: F 70 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.8461 (t80) REVERT: F 139 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7443 (mm-30) REVERT: F 424 LYS cc_start: 0.8446 (mmmt) cc_final: 0.7838 (mmtp) REVERT: E 7 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6772 (mm-30) REVERT: E 28 GLN cc_start: 0.6566 (OUTLIER) cc_final: 0.5794 (pm20) REVERT: E 249 SER cc_start: 0.6790 (m) cc_final: 0.5764 (p) REVERT: E 402 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6849 (pm20) outliers start: 69 outliers final: 42 residues processed: 262 average time/residue: 0.3158 time to fit residues: 130.5023 Evaluate side-chains 251 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 192 time to evaluate : 2.021 ------------------------------------------------------------------------------- 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 141 CYS Chi-restraints excluded: chain A residue 187 TRP 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 70 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 197 THR 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 301 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 321 THR 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 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 105 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 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 315 VAL Chi-restraints excluded: chain F residue 379 ASN 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 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 Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 67 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 233 optimal weight: 0.9980 chunk 195 optimal weight: 0.9990 chunk 87 optimal weight: 0.0020 chunk 135 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS D 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.199964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.154098 restraints weight = 21932.176| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.44 r_work: 0.3187 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2495 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= 0.104 Angle : 0.471 7.407 28584 Z= 0.246 Chirality : 0.039 0.139 3108 Planarity : 0.004 0.056 3774 Dihedral : 3.652 19.666 2942 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.29 % Favored : 93.42 % Rotamer: Outliers : 3.45 % Allowed : 21.46 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.16), residues: 2736 helix: 2.08 (0.14), residues: 1386 sheet: -0.42 (0.35), residues: 255 loop : -1.14 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 187 HIS 0.008 0.001 HIS D 211 PHE 0.016 0.001 PHE C 219 TYR 0.010 0.001 TYR E 235 ARG 0.002 0.000 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 1153) hydrogen bonds : angle 4.01757 ( 3390) covalent geometry : bond 0.00229 (21114) covalent geometry : angle 0.47093 (28584) *********************** 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 265 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 193 time to evaluate : 2.200 Fit side-chains REVERT: A 105 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7927 (mm) REVERT: A 283 LYS cc_start: 0.5368 (OUTLIER) cc_final: 0.4608 (mttm) REVERT: A 347 MET cc_start: 0.4254 (mmm) cc_final: 0.2425 (tpp) REVERT: A 417 GLN cc_start: 0.7750 (tp40) cc_final: 0.7542 (tp40) REVERT: B 70 PHE cc_start: 0.9494 (OUTLIER) cc_final: 0.9176 (t80) REVERT: B 105 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7972 (mm) REVERT: B 206 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7154 (tt0) REVERT: B 396 ARG cc_start: 0.8408 (mtp85) cc_final: 0.8005 (mtt180) REVERT: C 7 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6595 (mm-30) REVERT: C 70 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.8482 (t80) REVERT: C 206 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6119 (mm-30) REVERT: C 219 PHE cc_start: 0.5976 (OUTLIER) cc_final: 0.5396 (m-80) REVERT: C 226 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6577 (mm) REVERT: C 282 ARG cc_start: 0.4628 (OUTLIER) cc_final: 0.4208 (mpp-170) REVERT: D 105 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7799 (mm) REVERT: D 187 TRP cc_start: 0.9279 (OUTLIER) cc_final: 0.8650 (p-90) REVERT: D 424 LYS cc_start: 0.8246 (mtpt) cc_final: 0.8040 (mmtp) REVERT: F 70 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.8486 (t80) REVERT: F 139 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7068 (mm-30) REVERT: F 424 LYS cc_start: 0.8340 (mmmt) cc_final: 0.7807 (mmtp) REVERT: E 7 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6658 (mm-30) REVERT: E 139 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6923 (mm-30) REVERT: E 249 SER cc_start: 0.6549 (m) cc_final: 0.5637 (p) REVERT: E 402 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6580 (pm20) outliers start: 72 outliers final: 46 residues processed: 258 average time/residue: 0.2989 time to fit residues: 122.5832 Evaluate side-chains 250 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 189 time to evaluate : 1.989 ------------------------------------------------------------------------------- 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 207 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 371 TRP 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 149 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 197 THR 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 321 THR 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 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 105 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 334 ILE 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 315 VAL Chi-restraints excluded: chain F residue 379 ASN 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 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 Chi-restraints excluded: chain E residue 402 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 58 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 263 optimal weight: 0.8980 chunk 260 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** 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 = 0.4133 r_free = 0.4133 target = 0.196659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.153730 restraints weight = 21960.385| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.46 r_work: 0.3157 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2537 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= 0.179 Angle : 0.544 7.031 28584 Z= 0.285 Chirality : 0.042 0.169 3108 Planarity : 0.004 0.058 3774 Dihedral : 3.955 19.492 2942 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.65 % Favored : 93.06 % Rotamer: Outliers : 3.64 % Allowed : 21.07 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.16), residues: 2736 helix: 1.87 (0.13), residues: 1386 sheet: -0.96 (0.32), residues: 288 loop : -1.16 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.008 0.001 HIS D 211 PHE 0.026 0.002 PHE D 219 TYR 0.014 0.001 TYR B 77 ARG 0.003 0.000 ARG B 361 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 1153) hydrogen bonds : angle 4.24183 ( 3390) covalent geometry : bond 0.00417 (21114) covalent geometry : angle 0.54385 (28584) *********************** 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 266 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 190 time to evaluate : 2.093 Fit side-chains revert: symmetry clash REVERT: A 24 SER cc_start: 0.7918 (t) cc_final: 0.7650 (p) REVERT: A 105 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8056 (mm) REVERT: A 150 VAL cc_start: 0.8464 (t) cc_final: 0.8201 (t) REVERT: A 283 LYS cc_start: 0.5247 (OUTLIER) cc_final: 0.4652 (mttm) REVERT: A 301 LEU cc_start: 0.4899 (OUTLIER) cc_final: 0.4540 (mm) REVERT: A 347 MET cc_start: 0.4376 (mmm) cc_final: 0.2441 (tpp) REVERT: B 70 PHE cc_start: 0.9532 (OUTLIER) cc_final: 0.9177 (t80) REVERT: B 105 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7884 (mm) REVERT: B 206 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: C 7 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6566 (mm-30) REVERT: C 70 PHE cc_start: 0.9506 (OUTLIER) cc_final: 0.8439 (t80) REVERT: C 149 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7571 (t0) REVERT: C 282 ARG cc_start: 0.4532 (OUTLIER) cc_final: 0.4212 (mpp-170) REVERT: D 187 TRP cc_start: 0.9270 (OUTLIER) cc_final: 0.8690 (p-90) REVERT: F 70 PHE cc_start: 0.9472 (OUTLIER) cc_final: 0.8488 (t80) REVERT: F 139 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7161 (mm-30) REVERT: F 424 LYS cc_start: 0.8314 (mmmt) cc_final: 0.7798 (mmtp) REVERT: E 7 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7335 (mm-30) REVERT: E 70 PHE cc_start: 0.9545 (OUTLIER) cc_final: 0.9291 (t80) REVERT: E 249 SER cc_start: 0.6474 (m) cc_final: 0.5648 (p) outliers start: 76 outliers final: 55 residues processed: 254 average time/residue: 0.3049 time to fit residues: 123.1002 Evaluate side-chains 255 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 186 time to evaluate : 2.333 ------------------------------------------------------------------------------- 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 249 SER Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 371 TRP 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 149 ASP Chi-restraints excluded: chain B residue 180 LEU 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 321 THR 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 341 ILE 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 334 ILE 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 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 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 70 PHE 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 Chi-restraints excluded: chain E residue 397 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 57 optimal weight: 0.0030 chunk 125 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 246 optimal weight: 30.0000 chunk 56 optimal weight: 0.0020 chunk 119 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 203 optimal weight: 10.0000 chunk 224 optimal weight: 0.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS D 69 GLN ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.197039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.152469 restraints weight = 21909.564| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.54 r_work: 0.3145 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 21114 Z= 0.149 Angle : 0.699 59.199 28584 Z= 0.392 Chirality : 0.041 0.437 3108 Planarity : 0.004 0.058 3774 Dihedral : 3.947 19.646 2942 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.80 % Favored : 92.91 % Rotamer: Outliers : 3.35 % Allowed : 21.50 % Favored : 75.14 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.16), residues: 2736 helix: 1.87 (0.13), residues: 1386 sheet: -0.99 (0.32), residues: 288 loop : -1.16 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 176 HIS 0.007 0.001 HIS D 211 PHE 0.033 0.002 PHE C 219 TYR 0.014 0.001 TYR B 77 ARG 0.003 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 1153) hydrogen bonds : angle 4.24012 ( 3390) covalent geometry : bond 0.00317 (21114) covalent geometry : angle 0.69871 (28584) ********************** REFINEMENT MACRO_CYCLE 10 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 257 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 187 time to evaluate : 2.114 Fit side-chains revert: symmetry clash REVERT: A 24 SER cc_start: 0.7904 (t) cc_final: 0.7620 (p) REVERT: A 105 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8034 (mm) REVERT: A 150 VAL cc_start: 0.8452 (t) cc_final: 0.8193 (t) REVERT: A 283 LYS cc_start: 0.5437 (OUTLIER) cc_final: 0.4792 (mttm) REVERT: A 301 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.4408 (mm) REVERT: A 347 MET cc_start: 0.4401 (mmm) cc_final: 0.2454 (tpp) REVERT: B 28 GLN cc_start: 0.6912 (pp30) cc_final: 0.6673 (pp30) REVERT: B 70 PHE cc_start: 0.9541 (OUTLIER) cc_final: 0.9185 (t80) REVERT: B 105 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7866 (mm) REVERT: B 206 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: C 7 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6525 (mm-30) REVERT: C 70 PHE cc_start: 0.9516 (OUTLIER) cc_final: 0.8435 (t80) REVERT: C 149 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7589 (t0) REVERT: C 282 ARG cc_start: 0.4462 (OUTLIER) cc_final: 0.4113 (mpp-170) REVERT: D 187 TRP cc_start: 0.9278 (OUTLIER) cc_final: 0.8654 (p-90) REVERT: F 70 PHE cc_start: 0.9488 (OUTLIER) cc_final: 0.8509 (t80) REVERT: F 139 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7111 (mm-30) REVERT: F 424 LYS cc_start: 0.8290 (mmmt) cc_final: 0.7752 (mmtp) REVERT: E 7 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7335 (mm-30) REVERT: E 28 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.6124 (mp10) REVERT: E 70 PHE cc_start: 0.9555 (OUTLIER) cc_final: 0.9306 (t80) REVERT: E 249 SER cc_start: 0.6500 (m) cc_final: 0.5613 (p) outliers start: 70 outliers final: 55 residues processed: 246 average time/residue: 0.3356 time to fit residues: 132.7658 Evaluate side-chains 255 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 185 time to evaluate : 2.152 ------------------------------------------------------------------------------- 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 207 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 371 TRP 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 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 321 THR 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 341 ILE 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 334 ILE 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 315 VAL Chi-restraints excluded: chain F residue 379 ASN 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 27 PHE Chi-restraints excluded: chain E residue 28 GLN Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 70 PHE 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 Chi-restraints excluded: chain E residue 397 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 223 optimal weight: 9.9990 chunk 263 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 57 optimal weight: 0.0980 chunk 70 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.197016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.154514 restraints weight = 22096.324| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.51 r_work: 0.3176 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 21114 Z= 0.149 Angle : 0.699 59.199 28584 Z= 0.392 Chirality : 0.041 0.437 3108 Planarity : 0.004 0.060 3774 Dihedral : 3.947 19.646 2942 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.80 % Favored : 92.91 % Rotamer: Outliers : 3.35 % Allowed : 21.70 % Favored : 74.95 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.16), residues: 2736 helix: 1.87 (0.13), residues: 1386 sheet: -0.99 (0.32), residues: 288 loop : -1.16 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 176 HIS 0.007 0.001 HIS D 211 PHE 0.033 0.002 PHE C 219 TYR 0.014 0.001 TYR B 77 ARG 0.003 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 1153) hydrogen bonds : angle 4.24012 ( 3390) covalent geometry : bond 0.00317 (21114) covalent geometry : angle 0.69871 (28584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8887.78 seconds wall clock time: 153 minutes 58.64 seconds (9238.64 seconds total)