Starting phenix.real_space_refine on Tue Nov 18 16:53:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mgl_23828/11_2025/7mgl_23828.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mgl_23828/11_2025/7mgl_23828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mgl_23828/11_2025/7mgl_23828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mgl_23828/11_2025/7mgl_23828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mgl_23828/11_2025/7mgl_23828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mgl_23828/11_2025/7mgl_23828.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 104 5.16 5 C 10132 2.51 5 N 2564 2.21 5 O 2672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15476 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3805 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 13, 'TRANS': 458} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'3PE': 1, 'ZB4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Restraints were copied for chains: B, C, D Time building chain proxies: 3.81, per 1000 atoms: 0.25 Number of scatterers: 15476 At special positions: 0 Unit cell: (112.86, 112.86, 110.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 4 15.00 O 2672 8.00 N 2564 7.00 C 10132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 166 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.04 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 766.5 milliseconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 64.0% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 removed outlier: 4.236A pdb=" N ARG A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.696A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 143 Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 290 through 293 removed outlier: 3.651A pdb=" N GLY A 293 " --> pdb=" O PHE A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 294 through 338 removed outlier: 4.319A pdb=" N ARG A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 337 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.598A pdb=" N GLU A 349 " --> pdb=" O TRP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 378 removed outlier: 3.604A pdb=" N ILE A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 removed outlier: 3.965A pdb=" N CYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 408 through 448 removed outlier: 3.852A pdb=" N LEU A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Proline residue: A 423 - end of helix Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.704A pdb=" N ARG A 455 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 472 through 482 Processing helix chain 'A' and resid 487 through 508 removed outlier: 3.531A pdb=" N MET A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 525 Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.695A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 143 Proline residue: B 140 - end of helix Processing helix chain 'B' and resid 290 through 293 removed outlier: 3.651A pdb=" N GLY B 293 " --> pdb=" O PHE B 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 290 through 293' Processing helix chain 'B' and resid 294 through 338 removed outlier: 4.319A pdb=" N ARG B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 removed outlier: 3.597A pdb=" N GLU B 349 " --> pdb=" O TRP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 378 removed outlier: 3.604A pdb=" N ILE B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 377 " --> pdb=" O ILE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 400 removed outlier: 3.964A pdb=" N CYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 Processing helix chain 'B' and resid 408 through 448 removed outlier: 3.852A pdb=" N LEU B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Proline residue: B 423 - end of helix Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.704A pdb=" N ARG B 455 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 472 through 482 Processing helix chain 'B' and resid 487 through 508 removed outlier: 3.532A pdb=" N MET B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 525 Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 51 through 59 Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.696A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 143 Proline residue: C 140 - end of helix Processing helix chain 'C' and resid 290 through 293 removed outlier: 3.651A pdb=" N GLY C 293 " --> pdb=" O PHE C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 290 through 293' Processing helix chain 'C' and resid 294 through 338 removed outlier: 4.318A pdb=" N ARG C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU C 299 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN C 337 " --> pdb=" O PHE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.597A pdb=" N GLU C 349 " --> pdb=" O TRP C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 378 removed outlier: 3.604A pdb=" N ILE C 356 " --> pdb=" O ASN C 352 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 377 " --> pdb=" O ILE C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 400 removed outlier: 3.965A pdb=" N CYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 Processing helix chain 'C' and resid 408 through 448 removed outlier: 3.852A pdb=" N LEU C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Proline residue: C 423 - end of helix Processing helix chain 'C' and resid 451 through 455 removed outlier: 3.705A pdb=" N ARG C 455 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 468 Processing helix chain 'C' and resid 472 through 482 Processing helix chain 'C' and resid 487 through 508 removed outlier: 3.531A pdb=" N MET C 508 " --> pdb=" O LEU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 525 Processing helix chain 'D' and resid 41 through 50 Processing helix chain 'D' and resid 51 through 59 Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.695A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 143 Proline residue: D 140 - end of helix Processing helix chain 'D' and resid 290 through 293 removed outlier: 3.651A pdb=" N GLY D 293 " --> pdb=" O PHE D 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 290 through 293' Processing helix chain 'D' and resid 294 through 338 removed outlier: 4.319A pdb=" N ARG D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU D 299 " --> pdb=" O ASN D 295 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN D 337 " --> pdb=" O PHE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 removed outlier: 3.599A pdb=" N GLU D 349 " --> pdb=" O TRP D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 378 removed outlier: 3.604A pdb=" N ILE D 356 " --> pdb=" O ASN D 352 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D 377 " --> pdb=" O ILE D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 400 removed outlier: 3.964A pdb=" N CYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 408 through 448 removed outlier: 3.851A pdb=" N LEU D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Proline residue: D 423 - end of helix Processing helix chain 'D' and resid 451 through 455 removed outlier: 3.704A pdb=" N ARG D 455 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 468 Processing helix chain 'D' and resid 472 through 482 Processing helix chain 'D' and resid 487 through 508 removed outlier: 3.531A pdb=" N MET D 508 " --> pdb=" O LEU D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 525 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 6.790A pdb=" N ARG A 168 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL A 231 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS A 166 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A 233 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA A 164 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N MET A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.790A pdb=" N ARG B 168 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL B 231 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS B 166 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE B 233 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 164 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N MET B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 119 removed outlier: 6.790A pdb=" N ARG C 168 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL C 231 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS C 166 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE C 233 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA C 164 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N MET C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 119 removed outlier: 6.791A pdb=" N ARG D 168 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL D 231 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS D 166 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE D 233 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA D 164 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N MET D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) 1064 hydrogen bonds defined for protein. 3132 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: 2.92 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4738 1.34 - 1.46: 3917 1.46 - 1.58: 7041 1.58 - 1.71: 8 1.71 - 1.83: 156 Bond restraints: 15860 Sorted by residual: bond pdb=" O02 ZB4 D 601 " pdb=" S01 ZB4 D 601 " ideal model delta sigma weight residual 1.454 1.779 -0.325 2.00e-02 2.50e+03 2.63e+02 bond pdb=" O02 ZB4 C 900 " pdb=" S01 ZB4 C 900 " ideal model delta sigma weight residual 1.454 1.778 -0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" O02 ZB4 A 601 " pdb=" S01 ZB4 A 601 " ideal model delta sigma weight residual 1.454 1.778 -0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" O02 ZB4 B 601 " pdb=" S01 ZB4 B 601 " ideal model delta sigma weight residual 1.454 1.778 -0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" O01 ZB4 B 601 " pdb=" S01 ZB4 B 601 " ideal model delta sigma weight residual 1.454 1.769 -0.315 2.00e-02 2.50e+03 2.48e+02 ... (remaining 15855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 21063 2.49 - 4.98: 346 4.98 - 7.48: 55 7.48 - 9.97: 24 9.97 - 12.46: 8 Bond angle restraints: 21496 Sorted by residual: angle pdb=" C GLU C 249 " pdb=" N ILE C 250 " pdb=" CA ILE C 250 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.15e+01 angle pdb=" C18 ZB4 C 900 " pdb=" O03 ZB4 C 900 " pdb=" C23 ZB4 C 900 " ideal model delta sigma weight residual 118.87 106.41 12.46 3.00e+00 1.11e-01 1.73e+01 angle pdb=" C18 ZB4 A 601 " pdb=" O03 ZB4 A 601 " pdb=" C23 ZB4 A 601 " ideal model delta sigma weight residual 118.87 106.42 12.45 3.00e+00 1.11e-01 1.72e+01 angle pdb=" C18 ZB4 D 601 " pdb=" O03 ZB4 D 601 " pdb=" C23 ZB4 D 601 " ideal model delta sigma weight residual 118.87 106.44 12.43 3.00e+00 1.11e-01 1.72e+01 angle pdb=" C18 ZB4 B 601 " pdb=" O03 ZB4 B 601 " pdb=" C23 ZB4 B 601 " ideal model delta sigma weight residual 118.87 106.47 12.40 3.00e+00 1.11e-01 1.71e+01 ... (remaining 21491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 8129 17.01 - 34.03: 928 34.03 - 51.04: 223 51.04 - 68.06: 64 68.06 - 85.07: 24 Dihedral angle restraints: 9368 sinusoidal: 3840 harmonic: 5528 Sorted by residual: dihedral pdb=" CB CYS B 253 " pdb=" SG CYS B 253 " pdb=" SG CYS B 284 " pdb=" CB CYS B 284 " ideal model delta sinusoidal sigma weight residual 93.00 21.90 71.10 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS D 253 " pdb=" SG CYS D 253 " pdb=" SG CYS D 284 " pdb=" CB CYS D 284 " ideal model delta sinusoidal sigma weight residual 93.00 21.91 71.09 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS A 253 " pdb=" SG CYS A 253 " pdb=" SG CYS A 284 " pdb=" CB CYS A 284 " ideal model delta sinusoidal sigma weight residual 93.00 21.93 71.07 1 1.00e+01 1.00e-02 6.49e+01 ... (remaining 9365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2111 0.064 - 0.128: 304 0.128 - 0.191: 13 0.191 - 0.255: 0 0.255 - 0.319: 4 Chirality restraints: 2432 Sorted by residual: chirality pdb=" C07 ZB4 C 900 " pdb=" C08 ZB4 C 900 " pdb=" C12 ZB4 C 900 " pdb=" N01 ZB4 C 900 " both_signs ideal model delta sigma weight residual False -2.52 -2.84 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C07 ZB4 A 601 " pdb=" C08 ZB4 A 601 " pdb=" C12 ZB4 A 601 " pdb=" N01 ZB4 A 601 " both_signs ideal model delta sigma weight residual False -2.52 -2.84 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C07 ZB4 B 601 " pdb=" C08 ZB4 B 601 " pdb=" C12 ZB4 B 601 " pdb=" N01 ZB4 B 601 " both_signs ideal model delta sigma weight residual False -2.52 -2.84 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 2429 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 62 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO C 63 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 63 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 63 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 62 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO B 63 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 63 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 63 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 62 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO D 63 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 63 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 63 " -0.029 5.00e-02 4.00e+02 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 637 2.72 - 3.27: 15232 3.27 - 3.81: 24754 3.81 - 4.36: 30356 4.36 - 4.90: 52229 Nonbonded interactions: 123208 Sorted by model distance: nonbonded pdb=" NH2 ARG C 455 " pdb=" OE2 GLU D 95 " model vdw 2.177 3.120 nonbonded pdb=" OD1 ASP D 134 " pdb=" OH TYR D 218 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASP A 134 " pdb=" OH TYR A 218 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASP C 134 " pdb=" OH TYR C 218 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASP B 134 " pdb=" OH TYR B 218 " model vdw 2.261 3.040 ... (remaining 123203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 601) selection = (chain 'B' and resid 40 through 601) selection = chain 'C' selection = (chain 'D' and resid 40 through 601) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.830 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.013 0.325 15868 Z= 0.638 Angle : 0.840 12.461 21512 Z= 0.426 Chirality : 0.044 0.319 2432 Planarity : 0.004 0.053 2640 Dihedral : 15.845 85.074 5784 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.10 % Allowed : 4.52 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.17), residues: 1872 helix: 0.19 (0.14), residues: 1112 sheet: -1.09 (0.37), residues: 196 loop : -2.94 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 455 TYR 0.024 0.002 TYR A 254 PHE 0.011 0.001 PHE D 83 TRP 0.008 0.001 TRP D 398 HIS 0.005 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.01290 (15860) covalent geometry : angle 0.83748 (21496) SS BOND : bond 0.00343 ( 8) SS BOND : angle 2.62542 ( 16) hydrogen bonds : bond 0.10096 ( 996) hydrogen bonds : angle 5.62223 ( 3132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.5737 (mtpt) REVERT: A 174 HIS cc_start: 0.7357 (m170) cc_final: 0.6506 (t-90) REVERT: A 283 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6594 (mm-30) REVERT: A 322 ARG cc_start: 0.6226 (ttp-170) cc_final: 0.5941 (ttm170) REVERT: B 46 LYS cc_start: 0.6809 (OUTLIER) cc_final: 0.6089 (mmmt) REVERT: B 89 LEU cc_start: 0.8184 (tp) cc_final: 0.7979 (tm) REVERT: B 168 ARG cc_start: 0.6510 (mtm110) cc_final: 0.6215 (mtt180) REVERT: B 276 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7456 (mp0) REVERT: B 283 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6621 (mm-30) REVERT: B 322 ARG cc_start: 0.6304 (ttp-170) cc_final: 0.6014 (ttp-110) REVERT: C 46 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6100 (mmmt) REVERT: C 89 LEU cc_start: 0.8086 (tp) cc_final: 0.7853 (tm) REVERT: C 168 ARG cc_start: 0.6302 (mtm110) cc_final: 0.5983 (mtt90) REVERT: C 322 ARG cc_start: 0.6309 (ttp-170) cc_final: 0.6098 (ttp-110) REVERT: D 46 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6082 (mmmt) REVERT: D 89 LEU cc_start: 0.8137 (tp) cc_final: 0.7900 (tm) REVERT: D 168 ARG cc_start: 0.6494 (mtm110) cc_final: 0.6210 (mtt180) REVERT: D 176 ASP cc_start: 0.7190 (t0) cc_final: 0.6924 (t70) outliers start: 52 outliers final: 5 residues processed: 243 average time/residue: 0.5848 time to fit residues: 157.7192 Evaluate side-chains 141 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain D residue 46 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS B 131 HIS B 243 GLN B 267 HIS B 286 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS C 194 GLN C 243 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 481 GLN D 131 HIS D 194 GLN D 243 GLN D 267 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.170922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.126045 restraints weight = 15889.589| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.99 r_work: 0.3098 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15868 Z= 0.141 Angle : 0.576 8.524 21512 Z= 0.301 Chirality : 0.041 0.132 2432 Planarity : 0.004 0.048 2640 Dihedral : 10.376 79.464 2338 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.90 % Allowed : 10.48 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.20), residues: 1872 helix: 1.86 (0.15), residues: 1108 sheet: -0.37 (0.39), residues: 196 loop : -2.25 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 347 TYR 0.016 0.001 TYR C 436 PHE 0.014 0.001 PHE D 350 TRP 0.007 0.001 TRP A 398 HIS 0.007 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00294 (15860) covalent geometry : angle 0.57459 (21496) SS BOND : bond 0.00550 ( 8) SS BOND : angle 1.50374 ( 16) hydrogen bonds : bond 0.05704 ( 996) hydrogen bonds : angle 4.28804 ( 3132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.6666 (ptt) cc_final: 0.6120 (mtt) REVERT: A 174 HIS cc_start: 0.7447 (m170) cc_final: 0.6040 (t-90) REVERT: A 222 THR cc_start: 0.8896 (m) cc_final: 0.8661 (m) REVERT: A 283 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6728 (mm-30) REVERT: A 371 MET cc_start: 0.7762 (mtp) cc_final: 0.7504 (mtt) REVERT: B 168 ARG cc_start: 0.6794 (mtm110) cc_final: 0.6060 (mtt180) REVERT: B 283 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6903 (pm20) REVERT: B 322 ARG cc_start: 0.6419 (ttp-170) cc_final: 0.6104 (ttp-110) REVERT: B 467 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8718 (mt) REVERT: C 168 ARG cc_start: 0.6681 (mtm110) cc_final: 0.6039 (mtt180) REVERT: C 322 ARG cc_start: 0.6390 (ttp-170) cc_final: 0.6146 (ttp-110) REVERT: D 168 ARG cc_start: 0.6837 (mtm110) cc_final: 0.6110 (mtt180) REVERT: D 176 ASP cc_start: 0.7141 (t0) cc_final: 0.6667 (t70) REVERT: D 276 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: D 322 ARG cc_start: 0.6201 (ttp-170) cc_final: 0.5868 (ttp-110) REVERT: D 467 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8694 (mt) outliers start: 32 outliers final: 10 residues processed: 186 average time/residue: 0.5029 time to fit residues: 105.6500 Evaluate side-chains 154 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 467 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 78 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 267 HIS A 286 HIS ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN B 97 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 495 GLN C 97 ASN C 267 HIS C 286 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 495 GLN D 97 ASN D 286 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS D 495 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.159101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.112049 restraints weight = 16343.816| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.93 r_work: 0.2951 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15868 Z= 0.191 Angle : 0.626 7.484 21512 Z= 0.324 Chirality : 0.043 0.174 2432 Planarity : 0.004 0.043 2640 Dihedral : 9.916 68.419 2317 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.04 % Allowed : 11.67 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.20), residues: 1872 helix: 2.21 (0.15), residues: 1108 sheet: -0.13 (0.37), residues: 204 loop : -2.01 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.022 0.002 TYR C 254 PHE 0.017 0.001 PHE B 182 TRP 0.006 0.001 TRP D 398 HIS 0.007 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00446 (15860) covalent geometry : angle 0.62197 (21496) SS BOND : bond 0.01259 ( 8) SS BOND : angle 2.53287 ( 16) hydrogen bonds : bond 0.06923 ( 996) hydrogen bonds : angle 4.45221 ( 3132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.6897 (ptt) cc_final: 0.6424 (mtt) REVERT: A 89 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8024 (tm) REVERT: A 115 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6633 (p0) REVERT: A 174 HIS cc_start: 0.7301 (m170) cc_final: 0.5490 (t-90) REVERT: A 283 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6972 (pm20) REVERT: A 371 MET cc_start: 0.7883 (mtp) cc_final: 0.7632 (mtt) REVERT: B 50 MET cc_start: 0.7791 (mtt) cc_final: 0.7556 (mtm) REVERT: B 89 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7954 (tm) REVERT: B 115 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6650 (p0) REVERT: B 168 ARG cc_start: 0.6946 (mtm110) cc_final: 0.6063 (mtt180) REVERT: B 283 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6847 (pm20) REVERT: B 322 ARG cc_start: 0.6383 (ttp-170) cc_final: 0.6065 (ttp-110) REVERT: B 376 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6752 (mm-30) REVERT: B 467 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8697 (mt) REVERT: C 89 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7955 (tm) REVERT: C 115 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6621 (p0) REVERT: C 168 ARG cc_start: 0.6922 (mtm110) cc_final: 0.6079 (mtt180) REVERT: C 322 ARG cc_start: 0.6461 (ttp-170) cc_final: 0.6140 (ttp-110) REVERT: D 115 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6683 (p0) REVERT: D 168 ARG cc_start: 0.6956 (mtm110) cc_final: 0.6080 (mtt180) REVERT: D 176 ASP cc_start: 0.7066 (t0) cc_final: 0.6498 (t70) REVERT: D 322 ARG cc_start: 0.6267 (ttp-170) cc_final: 0.5967 (ttp-110) REVERT: D 467 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8723 (mt) outliers start: 51 outliers final: 24 residues processed: 196 average time/residue: 0.4632 time to fit residues: 103.2401 Evaluate side-chains 175 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 79 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 90 optimal weight: 0.4980 chunk 123 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 120 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS A 451 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS C 131 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.164095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.120338 restraints weight = 16245.248| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.79 r_work: 0.3056 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15868 Z= 0.133 Angle : 0.558 10.734 21512 Z= 0.288 Chirality : 0.040 0.185 2432 Planarity : 0.004 0.043 2640 Dihedral : 9.128 67.603 2317 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.56 % Allowed : 12.62 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.20), residues: 1872 helix: 2.56 (0.15), residues: 1108 sheet: -0.07 (0.37), residues: 208 loop : -1.68 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.015 0.001 TYR D 436 PHE 0.011 0.001 PHE B 182 TRP 0.006 0.001 TRP B 398 HIS 0.007 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00278 (15860) covalent geometry : angle 0.55004 (21496) SS BOND : bond 0.01246 ( 8) SS BOND : angle 3.57263 ( 16) hydrogen bonds : bond 0.05501 ( 996) hydrogen bonds : angle 4.11545 ( 3132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.6661 (ptt) cc_final: 0.6227 (mtt) REVERT: A 174 HIS cc_start: 0.7263 (m170) cc_final: 0.5467 (t70) REVERT: A 283 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6904 (pm20) REVERT: A 322 ARG cc_start: 0.6447 (ttp-170) cc_final: 0.6219 (ttp-170) REVERT: A 371 MET cc_start: 0.7718 (mtp) cc_final: 0.7504 (mtt) REVERT: B 89 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7783 (tm) REVERT: B 168 ARG cc_start: 0.6818 (mtm110) cc_final: 0.5972 (mtt180) REVERT: B 196 ASP cc_start: 0.7694 (t70) cc_final: 0.7422 (t0) REVERT: B 283 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6845 (pm20) REVERT: B 322 ARG cc_start: 0.6282 (ttp-170) cc_final: 0.5923 (ttp-110) REVERT: C 168 ARG cc_start: 0.6804 (mtm110) cc_final: 0.5993 (mpt180) REVERT: C 322 ARG cc_start: 0.6237 (ttp-170) cc_final: 0.5933 (ttp-110) REVERT: D 89 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7734 (tm) REVERT: D 168 ARG cc_start: 0.6797 (mtm110) cc_final: 0.5979 (mtt180) REVERT: D 176 ASP cc_start: 0.7078 (t0) cc_final: 0.6543 (t70) REVERT: D 196 ASP cc_start: 0.7720 (t70) cc_final: 0.7441 (t0) REVERT: D 276 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: D 322 ARG cc_start: 0.6214 (ttp-170) cc_final: 0.5865 (ttp-110) outliers start: 43 outliers final: 19 residues processed: 189 average time/residue: 0.4845 time to fit residues: 103.9664 Evaluate side-chains 167 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 105 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS B 451 HIS C 451 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.163748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.119691 restraints weight = 16148.535| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.86 r_work: 0.3064 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15868 Z= 0.151 Angle : 0.594 10.685 21512 Z= 0.304 Chirality : 0.041 0.234 2432 Planarity : 0.004 0.041 2640 Dihedral : 9.019 65.292 2316 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.86 % Allowed : 13.51 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.20), residues: 1872 helix: 2.64 (0.15), residues: 1108 sheet: -0.11 (0.38), residues: 200 loop : -1.65 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 347 TYR 0.017 0.001 TYR D 436 PHE 0.014 0.001 PHE B 182 TRP 0.006 0.001 TRP D 398 HIS 0.008 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00336 (15860) covalent geometry : angle 0.58095 (21496) SS BOND : bond 0.01129 ( 8) SS BOND : angle 4.59988 ( 16) hydrogen bonds : bond 0.05936 ( 996) hydrogen bonds : angle 4.18051 ( 3132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.6654 (ptt) cc_final: 0.6293 (mtt) REVERT: A 89 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7725 (tm) REVERT: A 283 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6838 (pm20) REVERT: A 322 ARG cc_start: 0.6354 (ttp-170) cc_final: 0.6135 (ttp-110) REVERT: A 371 MET cc_start: 0.7696 (mtp) cc_final: 0.7480 (mtt) REVERT: B 89 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7720 (tm) REVERT: B 168 ARG cc_start: 0.6748 (mtm110) cc_final: 0.5971 (mmt90) REVERT: B 283 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6715 (pm20) REVERT: B 322 ARG cc_start: 0.6241 (ttp-170) cc_final: 0.6011 (ttp-170) REVERT: B 467 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8607 (mt) REVERT: C 89 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7755 (tm) REVERT: C 115 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6543 (p0) REVERT: C 168 ARG cc_start: 0.6768 (mtm110) cc_final: 0.5967 (mpt180) REVERT: C 322 ARG cc_start: 0.6163 (ttp-170) cc_final: 0.5782 (ttp-110) REVERT: D 89 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7713 (tm) REVERT: D 115 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6580 (p0) REVERT: D 168 ARG cc_start: 0.6764 (mtm110) cc_final: 0.5999 (mmt90) REVERT: D 176 ASP cc_start: 0.7080 (t0) cc_final: 0.6535 (t70) REVERT: D 196 ASP cc_start: 0.7594 (t70) cc_final: 0.7301 (t0) REVERT: D 276 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: D 322 ARG cc_start: 0.6147 (ttp-170) cc_final: 0.5809 (ttp-110) REVERT: D 467 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8610 (mt) outliers start: 48 outliers final: 22 residues processed: 187 average time/residue: 0.4761 time to fit residues: 101.1088 Evaluate side-chains 171 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS B 451 HIS C 451 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.159578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.114927 restraints weight = 16247.525| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.89 r_work: 0.3144 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15868 Z= 0.214 Angle : 0.699 12.853 21512 Z= 0.355 Chirality : 0.045 0.273 2432 Planarity : 0.004 0.041 2640 Dihedral : 9.310 65.569 2316 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.98 % Allowed : 13.21 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.20), residues: 1872 helix: 2.51 (0.15), residues: 1108 sheet: -0.17 (0.38), residues: 200 loop : -1.77 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 455 TYR 0.019 0.002 TYR A 436 PHE 0.015 0.001 PHE B 182 TRP 0.006 0.001 TRP D 491 HIS 0.009 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00518 (15860) covalent geometry : angle 0.67932 (21496) SS BOND : bond 0.01819 ( 8) SS BOND : angle 6.15364 ( 16) hydrogen bonds : bond 0.07010 ( 996) hydrogen bonds : angle 4.37896 ( 3132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6948 (ptt) cc_final: 0.6591 (mtt) REVERT: A 89 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7868 (tm) REVERT: A 146 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7355 (tpp80) REVERT: A 371 MET cc_start: 0.7914 (mtp) cc_final: 0.7674 (mtt) REVERT: B 89 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7869 (tm) REVERT: B 115 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6669 (p0) REVERT: B 168 ARG cc_start: 0.6920 (mtm110) cc_final: 0.6062 (mtt180) REVERT: B 285 LYS cc_start: 0.6201 (mptt) cc_final: 0.5769 (mptt) REVERT: B 322 ARG cc_start: 0.6395 (ttp-170) cc_final: 0.6140 (ttp-170) REVERT: B 467 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8698 (mt) REVERT: C 89 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7871 (tm) REVERT: C 115 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6616 (p0) REVERT: C 168 ARG cc_start: 0.6916 (mtm110) cc_final: 0.6092 (mtt180) REVERT: C 285 LYS cc_start: 0.6238 (mptt) cc_final: 0.5655 (mptt) REVERT: C 322 ARG cc_start: 0.6383 (ttp-170) cc_final: 0.6069 (ttp-110) REVERT: D 89 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7865 (tm) REVERT: D 115 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6670 (p0) REVERT: D 168 ARG cc_start: 0.6895 (mtm110) cc_final: 0.6051 (mtt180) REVERT: D 196 ASP cc_start: 0.7631 (t70) cc_final: 0.7297 (t0) REVERT: D 276 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: D 285 LYS cc_start: 0.6415 (mptt) cc_final: 0.5845 (mptt) REVERT: D 322 ARG cc_start: 0.6297 (ttp-170) cc_final: 0.5956 (ttp-110) REVERT: D 467 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8673 (mt) outliers start: 50 outliers final: 29 residues processed: 177 average time/residue: 0.4946 time to fit residues: 98.9161 Evaluate side-chains 177 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 8 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 83 optimal weight: 0.0570 chunk 82 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS C 451 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.162833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.117924 restraints weight = 16050.743| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.95 r_work: 0.3075 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15868 Z= 0.145 Angle : 0.611 12.015 21512 Z= 0.313 Chirality : 0.042 0.281 2432 Planarity : 0.004 0.042 2640 Dihedral : 9.041 64.761 2316 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.62 % Allowed : 13.57 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.20), residues: 1872 helix: 2.69 (0.15), residues: 1108 sheet: 0.09 (0.39), residues: 200 loop : -1.68 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 347 TYR 0.015 0.001 TYR A 436 PHE 0.014 0.001 PHE B 182 TRP 0.006 0.001 TRP B 398 HIS 0.008 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00319 (15860) covalent geometry : angle 0.59564 (21496) SS BOND : bond 0.01062 ( 8) SS BOND : angle 4.96541 ( 16) hydrogen bonds : bond 0.05735 ( 996) hydrogen bonds : angle 4.14305 ( 3132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6700 (ptt) cc_final: 0.6398 (mtt) REVERT: A 89 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7754 (tm) REVERT: A 371 MET cc_start: 0.7791 (mtp) cc_final: 0.7588 (mtt) REVERT: B 50 MET cc_start: 0.7780 (mtt) cc_final: 0.7552 (mtm) REVERT: B 89 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7781 (tm) REVERT: B 168 ARG cc_start: 0.6782 (mtm110) cc_final: 0.5966 (mpt180) REVERT: B 285 LYS cc_start: 0.6313 (mptt) cc_final: 0.5864 (mptt) REVERT: B 322 ARG cc_start: 0.6309 (ttp-170) cc_final: 0.6087 (ttp-170) REVERT: B 467 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8656 (mt) REVERT: C 89 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7752 (tm) REVERT: C 168 ARG cc_start: 0.6814 (mtm110) cc_final: 0.6007 (mpt180) REVERT: C 285 LYS cc_start: 0.6201 (mptt) cc_final: 0.5752 (mptt) REVERT: C 322 ARG cc_start: 0.6315 (ttp-170) cc_final: 0.5943 (ttp-110) REVERT: D 89 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7751 (tm) REVERT: D 168 ARG cc_start: 0.6782 (mtm110) cc_final: 0.5980 (mpt180) REVERT: D 196 ASP cc_start: 0.7621 (t70) cc_final: 0.7344 (t0) REVERT: D 276 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: D 285 LYS cc_start: 0.6221 (mptt) cc_final: 0.5790 (mptt) REVERT: D 322 ARG cc_start: 0.6191 (ttp-170) cc_final: 0.5804 (ttp-110) REVERT: D 467 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8651 (mt) outliers start: 44 outliers final: 25 residues processed: 180 average time/residue: 0.4885 time to fit residues: 99.5769 Evaluate side-chains 172 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 107 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS B 451 HIS C 451 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.157516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.109707 restraints weight = 16380.559| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.99 r_work: 0.2940 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15868 Z= 0.246 Angle : 0.753 14.651 21512 Z= 0.382 Chirality : 0.047 0.345 2432 Planarity : 0.005 0.041 2640 Dihedral : 9.346 66.560 2316 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.92 % Allowed : 13.81 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.20), residues: 1872 helix: 2.43 (0.15), residues: 1108 sheet: 0.02 (0.39), residues: 200 loop : -1.81 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 455 TYR 0.020 0.002 TYR C 436 PHE 0.017 0.001 PHE B 182 TRP 0.007 0.001 TRP D 491 HIS 0.010 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00601 (15860) covalent geometry : angle 0.73378 (21496) SS BOND : bond 0.01719 ( 8) SS BOND : angle 6.31491 ( 16) hydrogen bonds : bond 0.07485 ( 996) hydrogen bonds : angle 4.46922 ( 3132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 128 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.7017 (ptt) cc_final: 0.6646 (mtt) REVERT: A 89 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7954 (tm) REVERT: A 176 ASP cc_start: 0.7364 (t0) cc_final: 0.6850 (t70) REVERT: A 371 MET cc_start: 0.8020 (mtp) cc_final: 0.7792 (mtt) REVERT: B 89 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7951 (tm) REVERT: B 168 ARG cc_start: 0.6979 (mtm110) cc_final: 0.6001 (mtt180) REVERT: B 285 LYS cc_start: 0.6427 (mptt) cc_final: 0.6188 (mptt) REVERT: B 322 ARG cc_start: 0.6450 (ttp-170) cc_final: 0.6208 (ttp-170) REVERT: C 89 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7958 (tm) REVERT: C 168 ARG cc_start: 0.7021 (mtm110) cc_final: 0.6018 (mtt180) REVERT: C 285 LYS cc_start: 0.6305 (mptt) cc_final: 0.5854 (mptt) REVERT: C 322 ARG cc_start: 0.6424 (ttp-170) cc_final: 0.6124 (ttp-110) REVERT: D 89 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7932 (tm) REVERT: D 168 ARG cc_start: 0.6989 (mtm110) cc_final: 0.6009 (mtt180) REVERT: D 276 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: D 285 LYS cc_start: 0.6295 (mptt) cc_final: 0.5823 (mptt) REVERT: D 322 ARG cc_start: 0.6303 (ttp-170) cc_final: 0.5901 (ttp-110) REVERT: D 467 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8782 (mt) outliers start: 49 outliers final: 30 residues processed: 167 average time/residue: 0.5003 time to fit residues: 94.4660 Evaluate side-chains 161 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 113 optimal weight: 0.9980 chunk 101 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS C 451 HIS ** D 327 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 = 0.3752 r_free = 0.3752 target = 0.163255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.118537 restraints weight = 16090.322| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.94 r_work: 0.3080 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15868 Z= 0.139 Angle : 0.630 16.827 21512 Z= 0.322 Chirality : 0.042 0.290 2432 Planarity : 0.004 0.043 2640 Dihedral : 8.927 66.348 2316 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.20 % Allowed : 14.05 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.20), residues: 1872 helix: 2.71 (0.15), residues: 1108 sheet: 0.26 (0.40), residues: 200 loop : -1.68 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 347 TYR 0.014 0.001 TYR C 436 PHE 0.014 0.001 PHE B 182 TRP 0.006 0.001 TRP B 398 HIS 0.007 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00295 (15860) covalent geometry : angle 0.61413 (21496) SS BOND : bond 0.01367 ( 8) SS BOND : angle 5.21067 ( 16) hydrogen bonds : bond 0.05624 ( 996) hydrogen bonds : angle 4.18089 ( 3132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6749 (ptt) cc_final: 0.6451 (mtt) REVERT: A 89 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7719 (tm) REVERT: A 285 LYS cc_start: 0.6561 (mptt) cc_final: 0.6088 (mptt) REVERT: A 371 MET cc_start: 0.7831 (mtp) cc_final: 0.7630 (mtt) REVERT: B 50 MET cc_start: 0.7739 (mtt) cc_final: 0.7503 (mtm) REVERT: B 89 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7746 (tm) REVERT: B 168 ARG cc_start: 0.6753 (mtm110) cc_final: 0.5901 (mpt180) REVERT: B 285 LYS cc_start: 0.6450 (mptt) cc_final: 0.6052 (mptt) REVERT: B 322 ARG cc_start: 0.6274 (ttp-170) cc_final: 0.6048 (ttp-170) REVERT: C 89 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7713 (tm) REVERT: C 168 ARG cc_start: 0.6783 (mtm110) cc_final: 0.5966 (mpt180) REVERT: C 285 LYS cc_start: 0.6243 (mptt) cc_final: 0.5920 (mptt) REVERT: C 322 ARG cc_start: 0.6259 (ttp-170) cc_final: 0.6020 (ttp-170) REVERT: D 89 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7726 (tm) REVERT: D 168 ARG cc_start: 0.6755 (mtm110) cc_final: 0.5925 (mpt180) REVERT: D 276 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: D 285 LYS cc_start: 0.6212 (mptt) cc_final: 0.5827 (mptt) REVERT: D 322 ARG cc_start: 0.6142 (ttp-170) cc_final: 0.5751 (ttp-110) REVERT: D 467 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8613 (mt) outliers start: 37 outliers final: 26 residues processed: 170 average time/residue: 0.5080 time to fit residues: 97.4782 Evaluate side-chains 167 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 138 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS B 451 HIS C 451 HIS D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.165443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120241 restraints weight = 16113.191| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.85 r_work: 0.3041 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15868 Z= 0.130 Angle : 0.612 15.407 21512 Z= 0.308 Chirality : 0.041 0.259 2432 Planarity : 0.004 0.041 2640 Dihedral : 8.609 62.084 2316 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.96 % Allowed : 14.46 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.20), residues: 1872 helix: 2.85 (0.15), residues: 1108 sheet: 0.10 (0.40), residues: 208 loop : -1.58 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 338 TYR 0.014 0.001 TYR C 436 PHE 0.014 0.001 PHE B 182 TRP 0.007 0.001 TRP A 398 HIS 0.006 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00273 (15860) covalent geometry : angle 0.59950 (21496) SS BOND : bond 0.01202 ( 8) SS BOND : angle 4.57265 ( 16) hydrogen bonds : bond 0.05223 ( 996) hydrogen bonds : angle 4.07724 ( 3132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6717 (ptt) cc_final: 0.6427 (mtt) REVERT: A 89 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7779 (tm) REVERT: A 285 LYS cc_start: 0.6552 (mptt) cc_final: 0.6132 (mptt) REVERT: B 89 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7778 (tm) REVERT: B 168 ARG cc_start: 0.6863 (mtm110) cc_final: 0.5984 (mpt180) REVERT: B 285 LYS cc_start: 0.6581 (mptt) cc_final: 0.6291 (mptt) REVERT: B 322 ARG cc_start: 0.6164 (ttp-170) cc_final: 0.5843 (ttp-110) REVERT: C 50 MET cc_start: 0.7777 (mtt) cc_final: 0.7555 (mtm) REVERT: C 89 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7793 (tm) REVERT: C 168 ARG cc_start: 0.6920 (mtm110) cc_final: 0.6064 (mpt180) REVERT: C 285 LYS cc_start: 0.6123 (mptt) cc_final: 0.5890 (mptt) REVERT: C 322 ARG cc_start: 0.6184 (ttp-170) cc_final: 0.5851 (ttp-110) REVERT: C 480 MET cc_start: 0.7604 (mmp) cc_final: 0.7245 (mmp) REVERT: D 50 MET cc_start: 0.7830 (mtt) cc_final: 0.7603 (mtm) REVERT: D 89 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7707 (tm) REVERT: D 168 ARG cc_start: 0.6844 (mtm110) cc_final: 0.6015 (mpt180) REVERT: D 276 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.6725 (mp0) REVERT: D 285 LYS cc_start: 0.6282 (mptt) cc_final: 0.6041 (mptt) REVERT: D 322 ARG cc_start: 0.6179 (ttp-170) cc_final: 0.5901 (ttp-170) outliers start: 33 outliers final: 20 residues processed: 161 average time/residue: 0.5111 time to fit residues: 92.8934 Evaluate side-chains 151 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 456 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 27 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 137 optimal weight: 0.0470 chunk 35 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 110 optimal weight: 0.0370 chunk 123 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.165850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.118676 restraints weight = 16024.112| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.98 r_work: 0.3173 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15868 Z= 0.126 Angle : 0.606 14.663 21512 Z= 0.306 Chirality : 0.040 0.251 2432 Planarity : 0.004 0.042 2640 Dihedral : 8.348 58.089 2316 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.67 % Allowed : 14.76 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.20), residues: 1872 helix: 2.91 (0.15), residues: 1108 sheet: 0.51 (0.40), residues: 200 loop : -1.59 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 338 TYR 0.014 0.001 TYR A 436 PHE 0.013 0.001 PHE B 182 TRP 0.007 0.001 TRP B 398 HIS 0.005 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00260 (15860) covalent geometry : angle 0.59373 (21496) SS BOND : bond 0.01304 ( 8) SS BOND : angle 4.42646 ( 16) hydrogen bonds : bond 0.05115 ( 996) hydrogen bonds : angle 4.07452 ( 3132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5426.39 seconds wall clock time: 93 minutes 11.81 seconds (5591.81 seconds total)