Starting phenix.real_space_refine on Sat Jun 14 03:40:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mgl_23828/06_2025/7mgl_23828.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mgl_23828/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mgl_23828/06_2025/7mgl_23828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mgl_23828/06_2025/7mgl_23828.map" model { file = "/net/cci-nas-00/data/ceres_data/7mgl_23828/06_2025/7mgl_23828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mgl_23828/06_2025/7mgl_23828.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.92, per 1000 atoms: 0.58 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: 3.68 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.41 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: 4.60 Time building geometry restraints manager: 4.33 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 526 or resid 601)) selection = (chain 'B' and (resid 40 through 526 or resid 601)) selection = chain 'C' selection = (chain 'D' and (resid 40 through 526 or resid 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 34.060 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.460 ------------------------------------------------------------------------------- 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 : 5.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (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 TRP 0.008 0.001 TRP D 398 HIS 0.005 0.001 HIS B 451 PHE 0.011 0.001 PHE D 83 TYR 0.024 0.002 TYR A 254 ARG 0.003 0.000 ARG D 455 Details of bonding type rmsd hydrogen bonds : bond 0.10096 ( 996) hydrogen bonds : angle 5.62223 ( 3132) SS BOND : bond 0.00343 ( 8) SS BOND : angle 2.62542 ( 16) covalent geometry : bond 0.01290 (15860) covalent geometry : angle 0.83748 (21496) *********************** 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 : 1.562 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: 1.1559 time to fit residues: 313.2849 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 : 1.572 ------------------------------------------------------------------------------- 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 158 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 chunk 96 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 147 optimal weight: 0.0980 chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.170071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.125336 restraints weight = 15948.029| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.00 r_work: 0.3125 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1383 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= 0.138 Angle : 0.577 7.761 21512 Z= 0.302 Chirality : 0.041 0.135 2432 Planarity : 0.004 0.049 2640 Dihedral : 10.592 80.483 2338 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.90 % Allowed : 10.54 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1872 helix: 1.81 (0.15), residues: 1108 sheet: -0.36 (0.39), residues: 196 loop : -2.29 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 398 HIS 0.007 0.001 HIS A 451 PHE 0.014 0.001 PHE D 350 TYR 0.016 0.001 TYR D 436 ARG 0.003 0.000 ARG C 347 Details of bonding type rmsd hydrogen bonds : bond 0.05695 ( 996) hydrogen bonds : angle 4.33159 ( 3132) SS BOND : bond 0.00891 ( 8) SS BOND : angle 1.65658 ( 16) covalent geometry : bond 0.00283 (15860) covalent geometry : angle 0.57499 (21496) *********************** 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 191 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.786 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.6620 (ptt) cc_final: 0.6041 (mtt) REVERT: A 174 HIS cc_start: 0.7480 (m170) cc_final: 0.6093 (t-90) REVERT: A 222 THR cc_start: 0.8877 (m) cc_final: 0.8632 (m) REVERT: A 283 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6773 (mm-30) REVERT: B 168 ARG cc_start: 0.6793 (mtm110) cc_final: 0.6055 (mtt180) REVERT: B 283 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6917 (pm20) REVERT: B 322 ARG cc_start: 0.6466 (ttp-170) cc_final: 0.6146 (ttp-110) REVERT: B 376 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6773 (mt-10) REVERT: C 168 ARG cc_start: 0.6668 (mtm110) cc_final: 0.6014 (mtt180) REVERT: C 322 ARG cc_start: 0.6457 (ttp-170) cc_final: 0.6210 (ttp-110) REVERT: D 168 ARG cc_start: 0.6851 (mtm110) cc_final: 0.6133 (mtt180) REVERT: D 176 ASP cc_start: 0.7139 (t0) cc_final: 0.6663 (t70) REVERT: D 276 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: D 322 ARG cc_start: 0.6241 (ttp-170) cc_final: 0.5910 (ttp-110) outliers start: 32 outliers final: 13 residues processed: 183 average time/residue: 1.2826 time to fit residues: 265.3275 Evaluate side-chains 153 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 2.763 ------------------------------------------------------------------------------- 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 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 11 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.156192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.108853 restraints weight = 16232.537| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.93 r_work: 0.2978 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 15868 Z= 0.270 Angle : 0.712 12.361 21512 Z= 0.365 Chirality : 0.047 0.179 2432 Planarity : 0.005 0.044 2640 Dihedral : 10.174 67.445 2317 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.33 % Allowed : 11.73 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.19), residues: 1872 helix: 1.96 (0.15), residues: 1108 sheet: -0.12 (0.37), residues: 204 loop : -2.12 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 491 HIS 0.007 0.001 HIS B 451 PHE 0.019 0.002 PHE A 182 TYR 0.027 0.002 TYR C 254 ARG 0.004 0.001 ARG C 455 Details of bonding type rmsd hydrogen bonds : bond 0.08013 ( 996) hydrogen bonds : angle 4.64699 ( 3132) SS BOND : bond 0.01304 ( 8) SS BOND : angle 2.48883 ( 16) covalent geometry : bond 0.00663 (15860) covalent geometry : angle 0.70883 (21496) *********************** 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 201 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 145 time to evaluate : 2.447 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.7040 (ptt) cc_final: 0.6464 (mtt) REVERT: A 146 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7523 (tpp80) REVERT: A 174 HIS cc_start: 0.7371 (m170) cc_final: 0.5429 (t-90) REVERT: A 283 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7058 (pm20) REVERT: A 371 MET cc_start: 0.7995 (mtp) cc_final: 0.7747 (mtt) REVERT: B 89 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8083 (tm) REVERT: B 115 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6693 (p0) REVERT: B 168 ARG cc_start: 0.7034 (mtm110) cc_final: 0.6144 (mtt180) REVERT: B 283 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6959 (pm20) REVERT: B 322 ARG cc_start: 0.6495 (ttp-170) cc_final: 0.6148 (ttp-110) REVERT: B 467 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8744 (mt) REVERT: C 89 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8073 (tm) REVERT: C 115 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6652 (p0) REVERT: C 168 ARG cc_start: 0.7040 (mtm110) cc_final: 0.6195 (mtt180) REVERT: C 196 ASP cc_start: 0.7578 (t70) cc_final: 0.7362 (t70) REVERT: C 322 ARG cc_start: 0.6551 (ttp-170) cc_final: 0.6291 (ttp-110) REVERT: C 467 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8737 (mt) REVERT: D 89 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8087 (tm) REVERT: D 115 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6684 (p0) REVERT: D 168 ARG cc_start: 0.7049 (mtm110) cc_final: 0.6167 (mtt180) REVERT: D 176 ASP cc_start: 0.7175 (t0) cc_final: 0.6565 (t70) REVERT: D 276 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: D 322 ARG cc_start: 0.6346 (ttp-170) cc_final: 0.6032 (ttp-110) REVERT: D 467 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8769 (mt) outliers start: 56 outliers final: 25 residues processed: 195 average time/residue: 1.4445 time to fit residues: 324.9348 Evaluate side-chains 163 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 239 THR 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 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 239 THR Chi-restraints excluded: chain B residue 363 VAL 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 C residue 467 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 64 CYS 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 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 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 13 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 117 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 495 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.163858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.119921 restraints weight = 16030.193| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.87 r_work: 0.3055 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2155 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= 0.131 Angle : 0.569 11.150 21512 Z= 0.292 Chirality : 0.040 0.172 2432 Planarity : 0.004 0.044 2640 Dihedral : 9.438 67.711 2317 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.44 % Allowed : 12.80 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1872 helix: 2.44 (0.15), residues: 1108 sheet: 0.04 (0.37), residues: 204 loop : -1.80 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 398 HIS 0.007 0.001 HIS B 451 PHE 0.011 0.001 PHE A 182 TYR 0.014 0.001 TYR A 436 ARG 0.004 0.000 ARG B 347 Details of bonding type rmsd hydrogen bonds : bond 0.05561 ( 996) hydrogen bonds : angle 4.18003 ( 3132) SS BOND : bond 0.01241 ( 8) SS BOND : angle 3.52085 ( 16) covalent geometry : bond 0.00264 (15860) covalent geometry : angle 0.56134 (21496) *********************** 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 192 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.771 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.6610 (ptt) cc_final: 0.6148 (mtt) REVERT: A 89 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7769 (tm) REVERT: A 174 HIS cc_start: 0.7284 (m170) cc_final: 0.5420 (t-90) REVERT: A 283 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6914 (pm20) REVERT: A 371 MET cc_start: 0.7653 (mtp) cc_final: 0.7443 (mtt) REVERT: B 168 ARG cc_start: 0.6778 (mtm110) cc_final: 0.5981 (mpt180) REVERT: B 196 ASP cc_start: 0.7590 (t70) cc_final: 0.7284 (t0) REVERT: B 283 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6846 (pm20) REVERT: B 322 ARG cc_start: 0.6186 (ttp-170) cc_final: 0.5876 (ttp-110) REVERT: B 467 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8612 (mt) REVERT: C 89 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7803 (tm) REVERT: C 168 ARG cc_start: 0.6764 (mtm110) cc_final: 0.6011 (mtt180) REVERT: C 196 ASP cc_start: 0.7529 (t70) cc_final: 0.7263 (t0) REVERT: C 322 ARG cc_start: 0.6203 (ttp-170) cc_final: 0.5893 (ttp-110) REVERT: C 467 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8609 (mt) REVERT: D 168 ARG cc_start: 0.6783 (mtm110) cc_final: 0.6043 (mmt90) REVERT: D 176 ASP cc_start: 0.7057 (t0) cc_final: 0.6517 (t70) REVERT: D 196 ASP cc_start: 0.7629 (t70) cc_final: 0.7335 (t0) REVERT: D 276 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: D 322 ARG cc_start: 0.6122 (ttp-170) cc_final: 0.5769 (ttp-110) REVERT: D 467 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8597 (mt) outliers start: 41 outliers final: 14 residues processed: 184 average time/residue: 1.0046 time to fit residues: 210.2881 Evaluate side-chains 169 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 239 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 89 LEU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 467 LEU 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 467 LEU 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 54 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 136 optimal weight: 0.2980 chunk 35 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 451 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.166390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.122961 restraints weight = 16189.951| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.78 r_work: 0.3054 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2437 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= 0.124 Angle : 0.550 9.956 21512 Z= 0.284 Chirality : 0.040 0.210 2432 Planarity : 0.004 0.042 2640 Dihedral : 8.849 64.505 2316 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.20 % Allowed : 14.11 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.20), residues: 1872 helix: 2.72 (0.15), residues: 1108 sheet: 0.09 (0.38), residues: 200 loop : -1.58 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 398 HIS 0.006 0.001 HIS B 451 PHE 0.012 0.001 PHE B 182 TYR 0.015 0.001 TYR A 436 ARG 0.003 0.000 ARG B 347 Details of bonding type rmsd hydrogen bonds : bond 0.05097 ( 996) hydrogen bonds : angle 4.00834 ( 3132) SS BOND : bond 0.01273 ( 8) SS BOND : angle 4.09635 ( 16) covalent geometry : bond 0.00253 (15860) covalent geometry : angle 0.53887 (21496) *********************** 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 183 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 1.819 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.6632 (ptt) cc_final: 0.6287 (mtt) REVERT: A 89 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7780 (tm) REVERT: A 174 HIS cc_start: 0.7227 (m170) cc_final: 0.5346 (t70) REVERT: A 283 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6855 (pm20) REVERT: A 488 SER cc_start: 0.7670 (OUTLIER) cc_final: 0.7401 (p) REVERT: B 50 MET cc_start: 0.7792 (mtt) cc_final: 0.7565 (mtm) REVERT: B 89 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7766 (tm) REVERT: B 168 ARG cc_start: 0.6848 (mtm110) cc_final: 0.6064 (mmt90) REVERT: B 283 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6783 (pm20) REVERT: B 322 ARG cc_start: 0.6308 (ttp-170) cc_final: 0.5970 (ttp-110) REVERT: B 467 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8665 (mt) REVERT: C 89 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7776 (tm) REVERT: C 168 ARG cc_start: 0.6837 (mtm110) cc_final: 0.6018 (mtt180) REVERT: C 322 ARG cc_start: 0.6245 (ttp-170) cc_final: 0.5899 (ttp-110) REVERT: C 467 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8666 (mt) REVERT: D 89 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7754 (tm) REVERT: D 168 ARG cc_start: 0.6826 (mtm110) cc_final: 0.6003 (mpt180) REVERT: D 176 ASP cc_start: 0.7082 (t0) cc_final: 0.6577 (t70) REVERT: D 276 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: D 322 ARG cc_start: 0.6169 (ttp-170) cc_final: 0.5773 (ttp-110) REVERT: D 467 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8663 (mt) outliers start: 37 outliers final: 14 residues processed: 179 average time/residue: 1.0060 time to fit residues: 204.3241 Evaluate side-chains 161 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 321 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 161 SER 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 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 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 467 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 19 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.159028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.114280 restraints weight = 16300.772| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.88 r_work: 0.3006 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15868 Z= 0.237 Angle : 0.735 15.403 21512 Z= 0.371 Chirality : 0.046 0.302 2432 Planarity : 0.005 0.041 2640 Dihedral : 9.345 64.479 2316 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.68 % Allowed : 14.05 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.20), residues: 1872 helix: 2.49 (0.15), residues: 1108 sheet: -0.16 (0.38), residues: 200 loop : -1.77 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 491 HIS 0.009 0.001 HIS B 451 PHE 0.016 0.001 PHE B 182 TYR 0.021 0.002 TYR A 436 ARG 0.004 0.000 ARG B 455 Details of bonding type rmsd hydrogen bonds : bond 0.07318 ( 996) hydrogen bonds : angle 4.42704 ( 3132) SS BOND : bond 0.02046 ( 8) SS BOND : angle 6.90607 ( 16) covalent geometry : bond 0.00581 (15860) covalent geometry : angle 0.71034 (21496) *********************** 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 177 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6842 (ptt) cc_final: 0.6478 (mtt) REVERT: A 89 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7822 (tm) REVERT: B 89 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7805 (tm) REVERT: B 168 ARG cc_start: 0.6769 (mtm110) cc_final: 0.5878 (mtt180) REVERT: B 285 LYS cc_start: 0.6192 (mptt) cc_final: 0.5978 (mptt) REVERT: B 322 ARG cc_start: 0.6250 (ttp-170) cc_final: 0.5940 (ttp-110) REVERT: B 467 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8592 (mt) REVERT: C 89 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7812 (tm) REVERT: C 115 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6543 (p0) REVERT: C 168 ARG cc_start: 0.6817 (mtm110) cc_final: 0.5911 (mtt180) REVERT: C 285 LYS cc_start: 0.6253 (mptt) cc_final: 0.5691 (mptt) REVERT: C 322 ARG cc_start: 0.6268 (ttp-170) cc_final: 0.5956 (ttp-110) REVERT: C 467 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8594 (mt) REVERT: D 89 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7786 (tm) REVERT: D 168 ARG cc_start: 0.6792 (mtm110) cc_final: 0.5867 (mtt180) REVERT: D 276 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: D 285 LYS cc_start: 0.6362 (mptt) cc_final: 0.5805 (mptt) REVERT: D 322 ARG cc_start: 0.6173 (ttp-170) cc_final: 0.5842 (ttp-110) REVERT: D 467 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8588 (mt) outliers start: 45 outliers final: 26 residues processed: 171 average time/residue: 0.9937 time to fit residues: 192.7560 Evaluate side-chains 164 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 488 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 239 THR Chi-restraints excluded: chain B residue 310 SER 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 C residue 467 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 64 CYS 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 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 13 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 130 optimal weight: 0.0370 chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS C 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.165357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.120711 restraints weight = 16229.936| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.92 r_work: 0.3069 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2534 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= 0.134 Angle : 0.608 14.257 21512 Z= 0.310 Chirality : 0.042 0.290 2432 Planarity : 0.004 0.043 2640 Dihedral : 8.954 63.599 2316 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.26 % Allowed : 14.52 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.20), residues: 1872 helix: 2.71 (0.15), residues: 1108 sheet: 0.13 (0.39), residues: 200 loop : -1.66 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 398 HIS 0.007 0.001 HIS B 451 PHE 0.013 0.001 PHE B 182 TYR 0.014 0.001 TYR A 436 ARG 0.003 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.05389 ( 996) hydrogen bonds : angle 4.08869 ( 3132) SS BOND : bond 0.01356 ( 8) SS BOND : angle 5.22705 ( 16) covalent geometry : bond 0.00281 (15860) covalent geometry : angle 0.59131 (21496) *********************** 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 181 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6637 (ptt) cc_final: 0.6355 (mtt) REVERT: A 89 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7745 (tm) REVERT: B 50 MET cc_start: 0.7667 (mtt) cc_final: 0.7461 (mtm) REVERT: B 89 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7711 (tm) REVERT: B 168 ARG cc_start: 0.6789 (mtm110) cc_final: 0.5976 (mpt180) REVERT: B 285 LYS cc_start: 0.6313 (mptt) cc_final: 0.5902 (mptt) REVERT: B 322 ARG cc_start: 0.6189 (ttp-170) cc_final: 0.5963 (ttp-170) REVERT: B 467 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8636 (mt) REVERT: C 89 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7717 (tm) REVERT: C 168 ARG cc_start: 0.6809 (mtm110) cc_final: 0.5998 (mpt180) REVERT: C 285 LYS cc_start: 0.6255 (mptt) cc_final: 0.5817 (mptt) REVERT: C 322 ARG cc_start: 0.6198 (ttp-170) cc_final: 0.5845 (ttp-110) REVERT: C 467 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8637 (mt) REVERT: D 89 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7690 (tm) REVERT: D 168 ARG cc_start: 0.6769 (mtm110) cc_final: 0.5956 (mpt180) REVERT: D 276 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: D 285 LYS cc_start: 0.6184 (mptt) cc_final: 0.5759 (mptt) REVERT: D 322 ARG cc_start: 0.6085 (ttp-170) cc_final: 0.5705 (ttp-110) REVERT: D 467 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8629 (mt) outliers start: 38 outliers final: 20 residues processed: 173 average time/residue: 0.9486 time to fit residues: 187.0113 Evaluate side-chains 167 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 89 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 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 239 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 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 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 53 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.166835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.122355 restraints weight = 15997.574| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.95 r_work: 0.3134 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15868 Z= 0.125 Angle : 0.586 13.325 21512 Z= 0.298 Chirality : 0.041 0.251 2432 Planarity : 0.004 0.042 2640 Dihedral : 8.533 56.680 2316 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.14 % Allowed : 14.94 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.20), residues: 1872 helix: 2.88 (0.15), residues: 1108 sheet: 0.47 (0.40), residues: 200 loop : -1.60 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 398 HIS 0.006 0.001 HIS D 451 PHE 0.014 0.001 PHE B 182 TYR 0.014 0.001 TYR A 436 ARG 0.003 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.05039 ( 996) hydrogen bonds : angle 4.03749 ( 3132) SS BOND : bond 0.01670 ( 8) SS BOND : angle 3.89298 ( 16) covalent geometry : bond 0.00258 (15860) covalent geometry : angle 0.57699 (21496) *********************** 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 170 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6715 (ptt) cc_final: 0.6411 (mtt) REVERT: A 89 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7795 (tm) REVERT: A 285 LYS cc_start: 0.6429 (mptt) cc_final: 0.6202 (mptt) REVERT: A 376 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6609 (mm-30) REVERT: A 488 SER cc_start: 0.7687 (OUTLIER) cc_final: 0.7431 (p) REVERT: B 50 MET cc_start: 0.7827 (mtt) cc_final: 0.7627 (mtm) REVERT: B 89 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7789 (tm) REVERT: B 168 ARG cc_start: 0.6862 (mtm110) cc_final: 0.6032 (mpt180) REVERT: B 285 LYS cc_start: 0.6374 (mptt) cc_final: 0.6154 (mptt) REVERT: B 322 ARG cc_start: 0.6232 (ttp-170) cc_final: 0.5899 (ttp-110) REVERT: B 467 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8697 (mt) REVERT: C 168 ARG cc_start: 0.6869 (mtm110) cc_final: 0.6065 (mpt180) REVERT: C 285 LYS cc_start: 0.6123 (mptt) cc_final: 0.5866 (mptt) REVERT: C 322 ARG cc_start: 0.6275 (ttp-170) cc_final: 0.5935 (ttp-110) REVERT: C 467 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8707 (mt) REVERT: D 50 MET cc_start: 0.7900 (mtt) cc_final: 0.7624 (mtm) REVERT: D 89 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7766 (tm) REVERT: D 168 ARG cc_start: 0.6874 (mtm110) cc_final: 0.6040 (mpt180) REVERT: D 285 LYS cc_start: 0.6198 (mptt) cc_final: 0.5936 (mptt) REVERT: D 322 ARG cc_start: 0.6223 (ttp-170) cc_final: 0.5944 (ttp-170) REVERT: D 467 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8706 (mt) outliers start: 36 outliers final: 19 residues processed: 165 average time/residue: 0.9470 time to fit residues: 177.9267 Evaluate side-chains 153 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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 488 SER Chi-restraints excluded: chain B residue 89 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 467 LEU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 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 467 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 234 HIS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 84 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 chunk 116 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 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 C 451 HIS D 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.164689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.120049 restraints weight = 16125.621| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.96 r_work: 0.3176 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15868 Z= 0.135 Angle : 0.595 12.207 21512 Z= 0.303 Chirality : 0.041 0.245 2432 Planarity : 0.004 0.042 2640 Dihedral : 8.260 59.393 2316 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.14 % Allowed : 14.76 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.20), residues: 1872 helix: 2.89 (0.15), residues: 1108 sheet: 0.45 (0.39), residues: 208 loop : -1.56 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 398 HIS 0.007 0.001 HIS C 451 PHE 0.013 0.001 PHE B 182 TYR 0.016 0.001 TYR D 436 ARG 0.002 0.000 ARG D 338 Details of bonding type rmsd hydrogen bonds : bond 0.05396 ( 996) hydrogen bonds : angle 4.07421 ( 3132) SS BOND : bond 0.01315 ( 8) SS BOND : angle 3.92813 ( 16) covalent geometry : bond 0.00290 (15860) covalent geometry : angle 0.58575 (21496) *********************** 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 171 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6781 (ptt) cc_final: 0.6514 (mtt) REVERT: A 89 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7859 (tm) REVERT: A 285 LYS cc_start: 0.6487 (mptt) cc_final: 0.6118 (mptt) REVERT: B 50 MET cc_start: 0.7885 (mtt) cc_final: 0.7680 (mtm) REVERT: B 89 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7838 (tm) REVERT: B 168 ARG cc_start: 0.6908 (mtm110) cc_final: 0.6084 (mpt180) REVERT: B 285 LYS cc_start: 0.6348 (mptt) cc_final: 0.6130 (mptt) REVERT: B 322 ARG cc_start: 0.6267 (ttp-170) cc_final: 0.5940 (ttp-110) REVERT: B 467 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8704 (mt) REVERT: C 168 ARG cc_start: 0.6903 (mtm110) cc_final: 0.6110 (mpt180) REVERT: C 285 LYS cc_start: 0.6114 (mptt) cc_final: 0.5876 (mptt) REVERT: C 322 ARG cc_start: 0.6323 (ttp-170) cc_final: 0.5986 (ttp-110) REVERT: C 467 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8728 (mt) REVERT: D 89 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7815 (tm) REVERT: D 168 ARG cc_start: 0.6893 (mtm110) cc_final: 0.6093 (mpt180) REVERT: D 285 LYS cc_start: 0.6255 (mptt) cc_final: 0.6020 (mptt) REVERT: D 322 ARG cc_start: 0.6276 (ttp-170) cc_final: 0.5919 (ttp-110) REVERT: D 467 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8702 (mt) outliers start: 36 outliers final: 27 residues processed: 167 average time/residue: 0.9413 time to fit residues: 179.5942 Evaluate side-chains 165 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 488 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 310 SER 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 165 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 467 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 15 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 56 optimal weight: 0.0170 chunk 28 optimal weight: 20.0000 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 0.0000 chunk 97 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.1826 ------------------------------------------------------------------------------- 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 D 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.163670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.117477 restraints weight = 16094.992| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.00 r_work: 0.2969 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2761 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= 0.142 Angle : 0.602 11.901 21512 Z= 0.305 Chirality : 0.041 0.239 2432 Planarity : 0.004 0.041 2640 Dihedral : 7.981 57.365 2316 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.20 % Allowed : 14.64 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.20), residues: 1872 helix: 2.88 (0.15), residues: 1108 sheet: 0.46 (0.39), residues: 208 loop : -1.55 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 398 HIS 0.008 0.001 HIS C 451 PHE 0.014 0.001 PHE B 182 TYR 0.016 0.001 TYR D 436 ARG 0.002 0.000 ARG D 338 Details of bonding type rmsd hydrogen bonds : bond 0.05604 ( 996) hydrogen bonds : angle 4.11515 ( 3132) SS BOND : bond 0.01327 ( 8) SS BOND : angle 3.68315 ( 16) covalent geometry : bond 0.00310 (15860) covalent geometry : angle 0.59345 (21496) ********************** 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 176 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6694 (ptt) cc_final: 0.6466 (mtt) REVERT: A 89 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7787 (tm) REVERT: A 285 LYS cc_start: 0.6635 (mptt) cc_final: 0.6387 (mptt) REVERT: B 50 MET cc_start: 0.7759 (mtt) cc_final: 0.7555 (mtm) REVERT: B 89 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7754 (tm) REVERT: B 168 ARG cc_start: 0.6797 (mtm110) cc_final: 0.6062 (mpt180) REVERT: B 322 ARG cc_start: 0.6124 (ttp-170) cc_final: 0.5853 (ttp-170) REVERT: B 467 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8688 (mt) REVERT: C 89 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7794 (tm) REVERT: C 168 ARG cc_start: 0.6814 (mtm110) cc_final: 0.6085 (mpt180) REVERT: C 285 LYS cc_start: 0.6169 (mptt) cc_final: 0.5936 (mptt) REVERT: C 322 ARG cc_start: 0.6127 (ttp-170) cc_final: 0.5791 (ttp-110) REVERT: C 467 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8683 (mt) REVERT: D 50 MET cc_start: 0.7819 (mtt) cc_final: 0.7603 (mtm) REVERT: D 89 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7784 (tm) REVERT: D 168 ARG cc_start: 0.6794 (mtm110) cc_final: 0.6068 (mpt180) REVERT: D 285 LYS cc_start: 0.6281 (mptt) cc_final: 0.6017 (mptt) REVERT: D 322 ARG cc_start: 0.6105 (ttp-170) cc_final: 0.5759 (ttp-110) REVERT: D 467 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8676 (mt) outliers start: 37 outliers final: 27 residues processed: 170 average time/residue: 0.9568 time to fit residues: 185.1339 Evaluate side-chains 168 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 111 ASP 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 488 SER Chi-restraints excluded: chain A residue 492 LEU 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 310 SER 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 165 LEU 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 467 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 0.0170 chunk 175 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.161188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.113808 restraints weight = 16068.093| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.96 r_work: 0.3119 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15868 Z= 0.170 Angle : 0.641 12.585 21512 Z= 0.323 Chirality : 0.042 0.248 2432 Planarity : 0.004 0.041 2640 Dihedral : 8.086 59.683 2316 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.02 % Allowed : 14.88 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.20), residues: 1872 helix: 2.80 (0.15), residues: 1108 sheet: 0.37 (0.39), residues: 208 loop : -1.58 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 398 HIS 0.009 0.001 HIS D 451 PHE 0.014 0.001 PHE C 182 TYR 0.019 0.001 TYR A 436 ARG 0.002 0.000 ARG D 338 Details of bonding type rmsd hydrogen bonds : bond 0.06261 ( 996) hydrogen bonds : angle 4.22898 ( 3132) SS BOND : bond 0.01423 ( 8) SS BOND : angle 3.86142 ( 16) covalent geometry : bond 0.00392 (15860) covalent geometry : angle 0.63216 (21496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10576.86 seconds wall clock time: 183 minutes 54.46 seconds (11034.46 seconds total)