Starting phenix.real_space_refine on Wed Mar 4 19:01:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mgl_23828/03_2026/7mgl_23828.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mgl_23828/03_2026/7mgl_23828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mgl_23828/03_2026/7mgl_23828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mgl_23828/03_2026/7mgl_23828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mgl_23828/03_2026/7mgl_23828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mgl_23828/03_2026/7mgl_23828.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 104 5.16 5 C 10132 2.51 5 N 2564 2.21 5 O 2672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15476 Number of models: 1 Model: "" Number of chains: 8 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: "B" 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: "C" 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: "D" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'3PE': 2, 'ZB4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'ZB4': 1} Classifications: {'undetermined': 1} Chain: "D" 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 Time building chain proxies: 3.75, per 1000 atoms: 0.24 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 B 253 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS C 166 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.04 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 666.8 milliseconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 64.0% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 removed outlier: 4.236A pdb=" N ARG A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.696A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 143 Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 290 through 293 removed outlier: 3.651A pdb=" N GLY A 293 " --> pdb=" O PHE A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 294 through 338 removed outlier: 4.319A pdb=" N ARG A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 337 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.598A pdb=" N GLU A 349 " --> pdb=" O TRP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 378 removed outlier: 3.604A pdb=" N ILE A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 removed outlier: 3.965A pdb=" N CYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 408 through 448 removed outlier: 3.852A pdb=" N LEU A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Proline residue: A 423 - end of helix Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.704A pdb=" N ARG A 455 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 472 through 482 Processing helix chain 'A' and resid 487 through 508 removed outlier: 3.531A pdb=" N MET A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 525 Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.695A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 143 Proline residue: B 140 - end of helix Processing helix chain 'B' and resid 290 through 293 removed outlier: 3.651A pdb=" N GLY B 293 " --> pdb=" O PHE B 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 290 through 293' Processing helix chain 'B' and resid 294 through 338 removed outlier: 4.319A pdb=" N ARG B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 removed outlier: 3.597A pdb=" N GLU B 349 " --> pdb=" O TRP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 378 removed outlier: 3.604A pdb=" N ILE B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 377 " --> pdb=" O ILE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 400 removed outlier: 3.964A pdb=" N CYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 Processing helix chain 'B' and resid 408 through 448 removed outlier: 3.852A pdb=" N LEU B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Proline residue: B 423 - end of helix Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.704A pdb=" N ARG B 455 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 472 through 482 Processing helix chain 'B' and resid 487 through 508 removed outlier: 3.532A pdb=" N MET B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 525 Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 51 through 59 Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.696A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 143 Proline residue: C 140 - end of helix Processing helix chain 'C' and resid 290 through 293 removed outlier: 3.651A pdb=" N GLY C 293 " --> pdb=" O PHE C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 290 through 293' Processing helix chain 'C' and resid 294 through 338 removed outlier: 4.318A pdb=" N ARG C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU C 299 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN C 337 " --> pdb=" O PHE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.597A pdb=" N GLU C 349 " --> pdb=" O TRP C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 378 removed outlier: 3.604A pdb=" N ILE C 356 " --> pdb=" O ASN C 352 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 377 " --> pdb=" O ILE C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 400 removed outlier: 3.965A pdb=" N CYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 Processing helix chain 'C' and resid 408 through 448 removed outlier: 3.852A pdb=" N LEU C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Proline residue: C 423 - end of helix Processing helix chain 'C' and resid 451 through 455 removed outlier: 3.705A pdb=" N ARG C 455 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 468 Processing helix chain 'C' and resid 472 through 482 Processing helix chain 'C' and resid 487 through 508 removed outlier: 3.531A pdb=" N MET C 508 " --> pdb=" O LEU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 525 Processing helix chain 'D' and resid 41 through 50 Processing helix chain 'D' and resid 51 through 59 Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.695A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 143 Proline residue: D 140 - end of helix Processing helix chain 'D' and resid 290 through 293 removed outlier: 3.651A pdb=" N GLY D 293 " --> pdb=" O PHE D 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 290 through 293' Processing helix chain 'D' and resid 294 through 338 removed outlier: 4.319A pdb=" N ARG D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU D 299 " --> pdb=" O ASN D 295 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN D 337 " --> pdb=" O PHE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 removed outlier: 3.599A pdb=" N GLU D 349 " --> pdb=" O TRP D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 378 removed outlier: 3.604A pdb=" N ILE D 356 " --> pdb=" O ASN D 352 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D 377 " --> pdb=" O ILE D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 400 removed outlier: 3.964A pdb=" N CYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 408 through 448 removed outlier: 3.851A pdb=" N LEU D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Proline residue: D 423 - end of helix Processing helix chain 'D' and resid 451 through 455 removed outlier: 3.704A pdb=" N ARG D 455 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 468 Processing helix chain 'D' and resid 472 through 482 Processing helix chain 'D' and resid 487 through 508 removed outlier: 3.531A pdb=" N MET D 508 " --> pdb=" O LEU D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 525 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 6.790A pdb=" N ARG A 168 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL A 231 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS A 166 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A 233 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA A 164 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N MET A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.790A pdb=" N ARG B 168 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL B 231 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS B 166 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE B 233 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 164 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N MET B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 119 removed outlier: 6.790A pdb=" N ARG C 168 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL C 231 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS C 166 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE C 233 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA C 164 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N MET C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 119 removed outlier: 6.791A pdb=" N ARG D 168 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL D 231 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS D 166 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE D 233 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA D 164 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N MET D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) 1064 hydrogen bonds defined for protein. 3132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4738 1.34 - 1.46: 3917 1.46 - 1.58: 7041 1.58 - 1.71: 8 1.71 - 1.83: 156 Bond restraints: 15860 Sorted by residual: bond pdb=" O02 ZB4 D 601 " pdb=" S01 ZB4 D 601 " ideal model delta sigma weight residual 1.454 1.779 -0.325 2.00e-02 2.50e+03 2.63e+02 bond pdb=" O02 ZB4 C 900 " pdb=" S01 ZB4 C 900 " ideal model delta sigma weight residual 1.454 1.778 -0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" O02 ZB4 A 601 " pdb=" S01 ZB4 A 601 " ideal model delta sigma weight residual 1.454 1.778 -0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" O02 ZB4 B 601 " pdb=" S01 ZB4 B 601 " ideal model delta sigma weight residual 1.454 1.778 -0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" O01 ZB4 B 601 " pdb=" S01 ZB4 B 601 " ideal model delta sigma weight residual 1.454 1.769 -0.315 2.00e-02 2.50e+03 2.48e+02 ... (remaining 15855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 21063 2.49 - 4.98: 346 4.98 - 7.48: 55 7.48 - 9.97: 24 9.97 - 12.46: 8 Bond angle restraints: 21496 Sorted by residual: angle pdb=" C GLU C 249 " pdb=" N ILE C 250 " pdb=" CA ILE C 250 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.15e+01 angle pdb=" C18 ZB4 C 900 " pdb=" O03 ZB4 C 900 " pdb=" C23 ZB4 C 900 " ideal model delta sigma weight residual 118.87 106.41 12.46 3.00e+00 1.11e-01 1.73e+01 angle pdb=" C18 ZB4 A 601 " pdb=" O03 ZB4 A 601 " pdb=" C23 ZB4 A 601 " ideal model delta sigma weight residual 118.87 106.42 12.45 3.00e+00 1.11e-01 1.72e+01 angle pdb=" C18 ZB4 D 601 " pdb=" O03 ZB4 D 601 " pdb=" C23 ZB4 D 601 " ideal model delta sigma weight residual 118.87 106.44 12.43 3.00e+00 1.11e-01 1.72e+01 angle pdb=" C18 ZB4 B 601 " pdb=" O03 ZB4 B 601 " pdb=" C23 ZB4 B 601 " ideal model delta sigma weight residual 118.87 106.47 12.40 3.00e+00 1.11e-01 1.71e+01 ... (remaining 21491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 8129 17.01 - 34.03: 928 34.03 - 51.04: 223 51.04 - 68.06: 64 68.06 - 85.07: 24 Dihedral angle restraints: 9368 sinusoidal: 3840 harmonic: 5528 Sorted by residual: dihedral pdb=" CB CYS B 253 " pdb=" SG CYS B 253 " pdb=" SG CYS B 284 " pdb=" CB CYS B 284 " ideal model delta sinusoidal sigma weight residual 93.00 21.90 71.10 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS D 253 " pdb=" SG CYS D 253 " pdb=" SG CYS D 284 " pdb=" CB CYS D 284 " ideal model delta sinusoidal sigma weight residual 93.00 21.91 71.09 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS A 253 " pdb=" SG CYS A 253 " pdb=" SG CYS A 284 " pdb=" CB CYS A 284 " ideal model delta sinusoidal sigma weight residual 93.00 21.93 71.07 1 1.00e+01 1.00e-02 6.49e+01 ... (remaining 9365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2111 0.064 - 0.128: 304 0.128 - 0.191: 13 0.191 - 0.255: 0 0.255 - 0.319: 4 Chirality restraints: 2432 Sorted by residual: chirality pdb=" C07 ZB4 C 900 " pdb=" C08 ZB4 C 900 " pdb=" C12 ZB4 C 900 " pdb=" N01 ZB4 C 900 " both_signs ideal model delta sigma weight residual False -2.52 -2.84 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C07 ZB4 A 601 " pdb=" C08 ZB4 A 601 " pdb=" C12 ZB4 A 601 " pdb=" N01 ZB4 A 601 " both_signs ideal model delta sigma weight residual False -2.52 -2.84 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C07 ZB4 B 601 " pdb=" C08 ZB4 B 601 " pdb=" C12 ZB4 B 601 " pdb=" N01 ZB4 B 601 " both_signs ideal model delta sigma weight residual False -2.52 -2.84 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 2429 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 62 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO C 63 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 63 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 63 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 62 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO B 63 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 63 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 63 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 62 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO D 63 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 63 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 63 " -0.029 5.00e-02 4.00e+02 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 637 2.72 - 3.27: 15232 3.27 - 3.81: 24754 3.81 - 4.36: 30356 4.36 - 4.90: 52229 Nonbonded interactions: 123208 Sorted by model distance: nonbonded pdb=" NH2 ARG C 455 " pdb=" OE2 GLU D 95 " model vdw 2.177 3.120 nonbonded pdb=" OD1 ASP D 134 " pdb=" OH TYR D 218 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASP A 134 " pdb=" OH TYR A 218 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASP C 134 " pdb=" OH TYR C 218 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASP B 134 " pdb=" OH TYR B 218 " model vdw 2.261 3.040 ... (remaining 123203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 601) selection = (chain 'B' and resid 40 through 601) selection = chain 'C' selection = (chain 'D' and resid 40 through 601) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.050 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.325 15868 Z= 0.638 Angle : 0.840 12.461 21512 Z= 0.426 Chirality : 0.044 0.319 2432 Planarity : 0.004 0.053 2640 Dihedral : 15.845 85.074 5784 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.10 % Allowed : 4.52 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.17), residues: 1872 helix: 0.19 (0.14), residues: 1112 sheet: -1.09 (0.37), residues: 196 loop : -2.94 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 455 TYR 0.024 0.002 TYR A 254 PHE 0.011 0.001 PHE D 83 TRP 0.008 0.001 TRP D 398 HIS 0.005 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.01290 (15860) covalent geometry : angle 0.83748 (21496) SS BOND : bond 0.00343 ( 8) SS BOND : angle 2.62542 ( 16) hydrogen bonds : bond 0.10096 ( 996) hydrogen bonds : angle 5.62223 ( 3132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.634 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: 0.6227 (ttp-170) cc_final: 0.5941 (ttm170) REVERT: B 46 LYS cc_start: 0.6808 (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: 0.6015 (ttp-110) REVERT: C 46 LYS cc_start: 0.6752 (OUTLIER) cc_final: 0.6100 (mmmt) REVERT: C 89 LEU cc_start: 0.8086 (tp) cc_final: 0.7853 (tm) REVERT: C 168 ARG cc_start: 0.6302 (mtm110) cc_final: 0.5983 (mtt90) REVERT: C 322 ARG cc_start: 0.6309 (ttp-170) cc_final: 0.6098 (ttp-110) REVERT: D 46 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6082 (mmmt) REVERT: D 89 LEU cc_start: 0.8137 (tp) cc_final: 0.7900 (tm) REVERT: D 168 ARG cc_start: 0.6494 (mtm110) cc_final: 0.6210 (mtt180) REVERT: D 176 ASP cc_start: 0.7190 (t0) cc_final: 0.6924 (t70) outliers start: 52 outliers final: 5 residues processed: 243 average time/residue: 0.5393 time to fit residues: 145.7817 Evaluate side-chains 141 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain D residue 46 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS B 131 HIS B 243 GLN B 267 HIS B 286 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS C 194 GLN C 243 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 481 GLN D 131 HIS D 194 GLN D 243 GLN D 267 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.170922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.126050 restraints weight = 15889.580| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.99 r_work: 0.3098 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15868 Z= 0.141 Angle : 0.576 8.524 21512 Z= 0.301 Chirality : 0.041 0.132 2432 Planarity : 0.004 0.048 2640 Dihedral : 10.376 79.463 2338 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.90 % Allowed : 10.48 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.20), residues: 1872 helix: 1.86 (0.15), residues: 1108 sheet: -0.37 (0.39), residues: 196 loop : -2.25 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 347 TYR 0.016 0.001 TYR C 436 PHE 0.014 0.001 PHE D 350 TRP 0.007 0.001 TRP A 398 HIS 0.007 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00294 (15860) covalent geometry : angle 0.57459 (21496) SS BOND : bond 0.00550 ( 8) SS BOND : angle 1.50370 ( 16) hydrogen bonds : bond 0.05704 ( 996) hydrogen bonds : angle 4.28803 ( 3132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.6663 (ptt) cc_final: 0.6118 (mtt) REVERT: A 174 HIS cc_start: 0.7445 (m170) cc_final: 0.6038 (t-90) REVERT: A 222 THR cc_start: 0.8895 (m) cc_final: 0.8660 (m) REVERT: A 283 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6731 (mm-30) REVERT: A 371 MET cc_start: 0.7757 (mtp) cc_final: 0.7499 (mtt) REVERT: B 168 ARG cc_start: 0.6792 (mtm110) cc_final: 0.6057 (mtt180) REVERT: B 283 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6902 (pm20) REVERT: B 322 ARG cc_start: 0.6426 (ttp-170) cc_final: 0.6111 (ttp-110) REVERT: B 467 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8718 (mt) REVERT: C 168 ARG cc_start: 0.6680 (mtm110) cc_final: 0.6036 (mtt180) REVERT: C 322 ARG cc_start: 0.6393 (ttp-170) cc_final: 0.6149 (ttp-110) REVERT: D 168 ARG cc_start: 0.6835 (mtm110) cc_final: 0.6107 (mtt180) REVERT: D 176 ASP cc_start: 0.7140 (t0) cc_final: 0.6666 (t70) REVERT: D 276 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: D 322 ARG cc_start: 0.6206 (ttp-170) cc_final: 0.5872 (ttp-110) REVERT: D 467 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8693 (mt) outliers start: 32 outliers final: 10 residues processed: 186 average time/residue: 0.4843 time to fit residues: 101.6360 Evaluate side-chains 154 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 467 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 78 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 286 HIS ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 495 GLN C 131 HIS C 267 HIS C 286 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 495 GLN D 97 ASN D 286 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS D 495 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.160950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.116738 restraints weight = 16310.342| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.80 r_work: 0.3017 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15868 Z= 0.168 Angle : 0.595 7.801 21512 Z= 0.309 Chirality : 0.042 0.173 2432 Planarity : 0.004 0.042 2640 Dihedral : 9.860 68.696 2317 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.92 % Allowed : 11.67 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1872 helix: 2.28 (0.15), residues: 1108 sheet: -0.21 (0.37), residues: 208 loop : -1.94 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.019 0.002 TYR A 436 PHE 0.015 0.001 PHE B 182 TRP 0.006 0.001 TRP D 398 HIS 0.007 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00381 (15860) covalent geometry : angle 0.59198 (21496) SS BOND : bond 0.01214 ( 8) SS BOND : angle 2.44298 ( 16) hydrogen bonds : bond 0.06428 ( 996) hydrogen bonds : angle 4.34850 ( 3132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.6855 (ptt) cc_final: 0.6359 (mtt) REVERT: A 115 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6659 (p0) REVERT: A 174 HIS cc_start: 0.7323 (m170) cc_final: 0.5570 (t-90) REVERT: A 283 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6978 (pm20) REVERT: A 371 MET cc_start: 0.7853 (mtp) cc_final: 0.7623 (mtt) REVERT: B 115 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6729 (p0) REVERT: B 168 ARG cc_start: 0.6908 (mtm110) cc_final: 0.6112 (mtt180) REVERT: B 283 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6828 (pm20) REVERT: B 322 ARG cc_start: 0.6434 (ttp-170) cc_final: 0.6054 (ttp-110) REVERT: B 376 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6760 (mm-30) REVERT: B 467 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8716 (mt) REVERT: C 115 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6605 (p0) REVERT: C 168 ARG cc_start: 0.6855 (mtm110) cc_final: 0.6093 (mtt180) REVERT: C 322 ARG cc_start: 0.6478 (ttp-170) cc_final: 0.6163 (ttp-110) REVERT: D 115 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6685 (p0) REVERT: D 168 ARG cc_start: 0.6939 (mtm110) cc_final: 0.6107 (mtt180) REVERT: D 176 ASP cc_start: 0.7106 (t0) cc_final: 0.6579 (t70) REVERT: D 322 ARG cc_start: 0.6254 (ttp-170) cc_final: 0.5954 (ttp-110) REVERT: D 467 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8721 (mt) outliers start: 49 outliers final: 23 residues processed: 195 average time/residue: 0.4430 time to fit residues: 98.3153 Evaluate side-chains 173 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 79 optimal weight: 0.3980 chunk 140 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 451 HIS B 97 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS C 97 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.158419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.111334 restraints weight = 16377.539| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.93 r_work: 0.2943 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15868 Z= 0.205 Angle : 0.649 11.579 21512 Z= 0.332 Chirality : 0.044 0.200 2432 Planarity : 0.004 0.042 2640 Dihedral : 9.389 68.370 2317 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.75 % Allowed : 11.73 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1872 helix: 2.33 (0.15), residues: 1108 sheet: -0.22 (0.37), residues: 208 loop : -1.83 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 455 TYR 0.019 0.002 TYR D 436 PHE 0.016 0.001 PHE B 182 TRP 0.006 0.001 TRP B 398 HIS 0.009 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00487 (15860) covalent geometry : angle 0.64105 (21496) SS BOND : bond 0.01605 ( 8) SS BOND : angle 3.66485 ( 16) hydrogen bonds : bond 0.07029 ( 996) hydrogen bonds : angle 4.43103 ( 3132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 140 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6907 (ptt) cc_final: 0.6477 (mtt) REVERT: A 89 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7934 (tm) REVERT: A 115 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6618 (p0) REVERT: A 146 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7501 (tpp80) REVERT: A 283 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6937 (pm20) REVERT: A 371 MET cc_start: 0.7898 (mtp) cc_final: 0.7653 (mtt) REVERT: B 89 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7899 (tm) REVERT: B 115 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6629 (p0) REVERT: B 168 ARG cc_start: 0.6952 (mtm110) cc_final: 0.6054 (mtt180) REVERT: B 196 ASP cc_start: 0.7672 (t70) cc_final: 0.7430 (t70) REVERT: B 276 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: B 283 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6885 (pm20) REVERT: B 322 ARG cc_start: 0.6379 (ttp-170) cc_final: 0.6179 (ttp-170) REVERT: B 467 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8713 (mt) REVERT: C 89 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7898 (tm) REVERT: C 115 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.6584 (p0) REVERT: C 168 ARG cc_start: 0.6944 (mtm110) cc_final: 0.6049 (mtt180) REVERT: C 276 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: C 322 ARG cc_start: 0.6454 (ttp-170) cc_final: 0.6134 (ttp-110) REVERT: D 89 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7905 (tm) REVERT: D 115 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6649 (p0) REVERT: D 168 ARG cc_start: 0.6975 (mtm110) cc_final: 0.6057 (mtt180) REVERT: D 196 ASP cc_start: 0.7712 (t70) cc_final: 0.7477 (t70) REVERT: D 276 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: D 322 ARG cc_start: 0.6280 (ttp-170) cc_final: 0.5919 (ttp-110) REVERT: D 467 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8719 (mt) outliers start: 63 outliers final: 25 residues processed: 191 average time/residue: 0.4653 time to fit residues: 100.3677 Evaluate side-chains 170 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 146 ARG 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 331 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain 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 115 ASP Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 115 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 105 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.166682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.123109 restraints weight = 16113.502| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.87 r_work: 0.3129 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15868 Z= 0.126 Angle : 0.553 11.288 21512 Z= 0.285 Chirality : 0.040 0.205 2432 Planarity : 0.004 0.043 2640 Dihedral : 8.922 65.160 2316 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.14 % Allowed : 13.69 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.20), residues: 1872 helix: 2.64 (0.15), residues: 1108 sheet: 0.01 (0.38), residues: 196 loop : -1.63 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 347 TYR 0.013 0.001 TYR D 436 PHE 0.011 0.001 PHE A 182 TRP 0.007 0.001 TRP B 398 HIS 0.007 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00262 (15860) covalent geometry : angle 0.54203 (21496) SS BOND : bond 0.01355 ( 8) SS BOND : angle 4.08786 ( 16) hydrogen bonds : bond 0.05159 ( 996) hydrogen bonds : angle 4.03497 ( 3132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.6633 (ptt) cc_final: 0.6267 (mtt) REVERT: A 174 HIS cc_start: 0.7204 (m170) cc_final: 0.5417 (t70) REVERT: A 283 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6918 (pm20) REVERT: A 322 ARG cc_start: 0.6472 (ttp-170) cc_final: 0.6249 (ttp-110) REVERT: B 50 MET cc_start: 0.7891 (mtt) cc_final: 0.7636 (mtm) REVERT: B 89 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7728 (tm) REVERT: B 168 ARG cc_start: 0.6807 (mtm110) cc_final: 0.6045 (mpt180) REVERT: B 196 ASP cc_start: 0.7552 (t70) cc_final: 0.7322 (t0) REVERT: B 283 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6798 (pm20) REVERT: B 322 ARG cc_start: 0.6343 (ttp-170) cc_final: 0.6113 (ttp-170) REVERT: C 89 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7728 (tm) REVERT: C 168 ARG cc_start: 0.6831 (mtm110) cc_final: 0.6072 (mpt180) REVERT: C 322 ARG cc_start: 0.6278 (ttp-170) cc_final: 0.5900 (ttp-110) REVERT: D 168 ARG cc_start: 0.6823 (mtm110) cc_final: 0.6061 (mpt180) REVERT: D 176 ASP cc_start: 0.7145 (t0) cc_final: 0.6619 (t70) REVERT: D 276 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: D 322 ARG cc_start: 0.6217 (ttp-170) cc_final: 0.5810 (ttp-110) outliers start: 36 outliers final: 14 residues processed: 178 average time/residue: 0.4519 time to fit residues: 91.1724 Evaluate side-chains 158 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 239 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 89 LEU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 165 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 492 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 137 optimal weight: 0.0980 chunk 173 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.160548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.116205 restraints weight = 16241.635| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.80 r_work: 0.2987 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15868 Z= 0.193 Angle : 0.685 12.702 21512 Z= 0.348 Chirality : 0.044 0.275 2432 Planarity : 0.004 0.041 2640 Dihedral : 9.232 63.837 2316 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.26 % Allowed : 13.93 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.20), residues: 1872 helix: 2.58 (0.15), residues: 1108 sheet: -0.21 (0.37), residues: 200 loop : -1.70 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 338 TYR 0.019 0.002 TYR A 436 PHE 0.015 0.001 PHE B 182 TRP 0.005 0.001 TRP A 491 HIS 0.009 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00463 (15860) covalent geometry : angle 0.65967 (21496) SS BOND : bond 0.01601 ( 8) SS BOND : angle 6.75367 ( 16) hydrogen bonds : bond 0.06647 ( 996) hydrogen bonds : angle 4.29753 ( 3132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6811 (ptt) cc_final: 0.6458 (mtt) REVERT: A 89 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7815 (tm) REVERT: B 89 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7785 (tm) REVERT: B 168 ARG cc_start: 0.6861 (mtm110) cc_final: 0.5924 (mtt180) REVERT: B 285 LYS cc_start: 0.6145 (mptt) cc_final: 0.5706 (mptt) REVERT: B 322 ARG cc_start: 0.6319 (ttp-170) cc_final: 0.6078 (ttp-170) REVERT: B 467 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8665 (mt) REVERT: C 89 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7776 (tm) REVERT: C 168 ARG cc_start: 0.6889 (mtm110) cc_final: 0.5969 (mtt180) REVERT: C 285 LYS cc_start: 0.6035 (mptt) cc_final: 0.5508 (mptt) REVERT: C 322 ARG cc_start: 0.6295 (ttp-170) cc_final: 0.5915 (ttp-110) REVERT: D 89 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7811 (tm) REVERT: D 168 ARG cc_start: 0.6863 (mtm110) cc_final: 0.5932 (mtt180) REVERT: D 276 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: D 285 LYS cc_start: 0.6299 (mptt) cc_final: 0.5732 (mptt) REVERT: D 322 ARG cc_start: 0.6195 (ttp-170) cc_final: 0.5788 (ttp-110) REVERT: D 467 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8666 (mt) outliers start: 38 outliers final: 21 residues processed: 176 average time/residue: 0.4626 time to fit residues: 92.3666 Evaluate side-chains 169 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 492 LEU 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 234 HIS Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 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 8 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.157854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.110305 restraints weight = 16161.911| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.95 r_work: 0.2997 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2407 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= 0.234 Angle : 0.722 14.074 21512 Z= 0.366 Chirality : 0.046 0.314 2432 Planarity : 0.005 0.042 2640 Dihedral : 9.407 67.018 2316 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.80 % Allowed : 13.69 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.20), residues: 1872 helix: 2.42 (0.15), residues: 1108 sheet: -0.17 (0.38), residues: 200 loop : -1.81 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 455 TYR 0.019 0.002 TYR A 436 PHE 0.017 0.001 PHE B 182 TRP 0.006 0.001 TRP C 491 HIS 0.010 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00570 (15860) covalent geometry : angle 0.70592 (21496) SS BOND : bond 0.01671 ( 8) SS BOND : angle 5.58161 ( 16) hydrogen bonds : bond 0.07371 ( 996) hydrogen bonds : angle 4.45982 ( 3132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.7068 (ptt) cc_final: 0.6701 (mtt) REVERT: A 89 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7957 (tm) REVERT: A 176 ASP cc_start: 0.7416 (t0) cc_final: 0.6896 (t70) REVERT: B 89 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7948 (tm) REVERT: B 168 ARG cc_start: 0.7012 (mtm110) cc_final: 0.6065 (mtt180) REVERT: B 285 LYS cc_start: 0.6429 (mptt) cc_final: 0.5971 (mptt) REVERT: B 467 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8760 (mt) REVERT: C 89 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7955 (tm) REVERT: C 168 ARG cc_start: 0.7025 (mtm110) cc_final: 0.6088 (mtt180) REVERT: C 276 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: C 285 LYS cc_start: 0.6347 (mptt) cc_final: 0.5812 (mptt) REVERT: D 89 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7942 (tm) REVERT: D 168 ARG cc_start: 0.6995 (mtm110) cc_final: 0.6052 (mtt180) REVERT: D 276 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: D 285 LYS cc_start: 0.6432 (mptt) cc_final: 0.5902 (mptt) REVERT: D 322 ARG cc_start: 0.6347 (ttp-170) cc_final: 0.5938 (ttp-110) REVERT: D 467 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8761 (mt) outliers start: 47 outliers final: 26 residues processed: 168 average time/residue: 0.4911 time to fit residues: 92.6674 Evaluate side-chains 166 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 306 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.160022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.112460 restraints weight = 16279.644| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.97 r_work: 0.2973 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15868 Z= 0.180 Angle : 0.667 13.294 21512 Z= 0.340 Chirality : 0.044 0.301 2432 Planarity : 0.004 0.043 2640 Dihedral : 9.163 67.509 2316 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.44 % Allowed : 13.93 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 1872 helix: 2.53 (0.15), residues: 1108 sheet: 0.01 (0.39), residues: 200 loop : -1.78 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 338 TYR 0.017 0.001 TYR A 436 PHE 0.015 0.001 PHE C 182 TRP 0.006 0.001 TRP C 398 HIS 0.009 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00420 (15860) covalent geometry : angle 0.65271 (21496) SS BOND : bond 0.01629 ( 8) SS BOND : angle 5.00617 ( 16) hydrogen bonds : bond 0.06464 ( 996) hydrogen bonds : angle 4.32136 ( 3132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6965 (ptt) cc_final: 0.6619 (mtt) REVERT: A 89 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7862 (tm) REVERT: A 146 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7474 (tpp80) REVERT: B 89 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7877 (tm) REVERT: B 168 ARG cc_start: 0.6919 (mtm110) cc_final: 0.5943 (mtt180) REVERT: B 285 LYS cc_start: 0.6455 (mptt) cc_final: 0.6205 (mptt) REVERT: B 467 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8748 (mt) REVERT: C 89 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7858 (tm) REVERT: C 168 ARG cc_start: 0.6934 (mtm110) cc_final: 0.5959 (mtt180) REVERT: C 276 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: C 285 LYS cc_start: 0.6241 (mptt) cc_final: 0.5772 (mptt) REVERT: C 322 ARG cc_start: 0.6642 (ttp-170) cc_final: 0.6433 (ttp-110) REVERT: D 89 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7873 (tm) REVERT: D 168 ARG cc_start: 0.6925 (mtm110) cc_final: 0.5949 (mtt180) REVERT: D 276 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: D 285 LYS cc_start: 0.6299 (mptt) cc_final: 0.5828 (mptt) REVERT: D 322 ARG cc_start: 0.6280 (ttp-170) cc_final: 0.5875 (ttp-110) REVERT: D 467 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8741 (mt) outliers start: 41 outliers final: 23 residues processed: 166 average time/residue: 0.4600 time to fit residues: 86.1524 Evaluate side-chains 165 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 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 234 HIS Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 113 optimal weight: 0.9990 chunk 101 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.160504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.112897 restraints weight = 16101.346| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.02 r_work: 0.3112 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2569 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= 0.172 Angle : 0.648 12.187 21512 Z= 0.330 Chirality : 0.043 0.271 2432 Planarity : 0.004 0.042 2640 Dihedral : 8.983 68.056 2316 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.56 % Allowed : 13.93 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.20), residues: 1872 helix: 2.61 (0.15), residues: 1108 sheet: 0.14 (0.39), residues: 200 loop : -1.72 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 338 TYR 0.017 0.001 TYR A 436 PHE 0.015 0.001 PHE C 182 TRP 0.006 0.001 TRP B 398 HIS 0.009 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00395 (15860) covalent geometry : angle 0.63768 (21496) SS BOND : bond 0.01578 ( 8) SS BOND : angle 4.30844 ( 16) hydrogen bonds : bond 0.06322 ( 996) hydrogen bonds : angle 4.27526 ( 3132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6986 (ptt) cc_final: 0.6593 (mtt) REVERT: A 89 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7888 (tm) REVERT: A 146 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7455 (tpp80) REVERT: A 285 LYS cc_start: 0.6602 (mptt) cc_final: 0.6130 (mptt) REVERT: B 89 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7876 (tm) REVERT: B 168 ARG cc_start: 0.6947 (mtm110) cc_final: 0.6077 (mmt90) REVERT: B 285 LYS cc_start: 0.6649 (mptt) cc_final: 0.6233 (mptt) REVERT: B 467 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8739 (mt) REVERT: C 89 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7853 (tm) REVERT: C 168 ARG cc_start: 0.6964 (mtm110) cc_final: 0.6105 (mmt90) REVERT: C 276 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: C 285 LYS cc_start: 0.6321 (mptt) cc_final: 0.5977 (mptt) REVERT: D 89 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7873 (tm) REVERT: D 168 ARG cc_start: 0.6920 (mtm110) cc_final: 0.6059 (mpt180) REVERT: D 276 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: D 285 LYS cc_start: 0.6324 (mptt) cc_final: 0.5862 (mptt) REVERT: D 322 ARG cc_start: 0.6308 (ttp-170) cc_final: 0.5905 (ttp-110) REVERT: D 467 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8735 (mt) outliers start: 43 outliers final: 30 residues processed: 171 average time/residue: 0.4671 time to fit residues: 90.3756 Evaluate side-chains 174 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 234 HIS 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 64 CYS Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 234 HIS Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 334 MET 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 138 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 23 optimal weight: 0.0060 chunk 63 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.167150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.122964 restraints weight = 16103.673| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.95 r_work: 0.3148 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2875 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= 0.124 Angle : 0.577 13.094 21512 Z= 0.295 Chirality : 0.040 0.237 2432 Planarity : 0.004 0.043 2640 Dihedral : 8.548 65.529 2316 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.14 % Allowed : 14.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.20), residues: 1872 helix: 2.87 (0.15), residues: 1108 sheet: 0.50 (0.40), residues: 200 loop : -1.58 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 338 TYR 0.012 0.001 TYR B 497 PHE 0.013 0.001 PHE B 182 TRP 0.006 0.001 TRP B 398 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00256 (15860) covalent geometry : angle 0.56925 (21496) SS BOND : bond 0.01248 ( 8) SS BOND : angle 3.50129 ( 16) hydrogen bonds : bond 0.04816 ( 996) hydrogen bonds : angle 3.99664 ( 3132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6724 (ptt) cc_final: 0.6435 (mtt) REVERT: A 89 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7742 (tm) REVERT: A 196 ASP cc_start: 0.7548 (t70) cc_final: 0.7337 (t0) REVERT: A 285 LYS cc_start: 0.6690 (mptt) cc_final: 0.6303 (mptt) REVERT: B 50 MET cc_start: 0.7815 (mtt) cc_final: 0.7613 (mtm) REVERT: B 89 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7733 (tm) REVERT: B 168 ARG cc_start: 0.6793 (mtm110) cc_final: 0.5977 (mpt180) REVERT: B 285 LYS cc_start: 0.6686 (mptt) cc_final: 0.6398 (mptt) REVERT: B 480 MET cc_start: 0.7559 (mmp) cc_final: 0.7261 (mmp) REVERT: C 50 MET cc_start: 0.7807 (mtt) cc_final: 0.7581 (mtm) REVERT: C 89 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7710 (tm) REVERT: C 168 ARG cc_start: 0.6796 (mtm110) cc_final: 0.6002 (mpt180) REVERT: C 285 LYS cc_start: 0.6215 (mptt) cc_final: 0.6004 (mptt) REVERT: C 480 MET cc_start: 0.7524 (mmp) cc_final: 0.7154 (mmp) REVERT: D 89 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7745 (tm) REVERT: D 168 ARG cc_start: 0.6774 (mtm110) cc_final: 0.5980 (mpt180) REVERT: D 285 LYS cc_start: 0.6333 (mptt) cc_final: 0.6053 (mptt) REVERT: D 322 ARG cc_start: 0.6183 (ttp-170) cc_final: 0.5815 (ttp-110) outliers start: 36 outliers final: 21 residues processed: 167 average time/residue: 0.4620 time to fit residues: 87.8237 Evaluate side-chains 158 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 B residue 89 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 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 D residue 89 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 27 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 137 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 123 optimal weight: 0.5980 chunk 163 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.166053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121231 restraints weight = 15985.308| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.83 r_work: 0.3097 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15868 Z= 0.127 Angle : 0.586 13.175 21512 Z= 0.298 Chirality : 0.040 0.230 2432 Planarity : 0.004 0.042 2640 Dihedral : 8.350 62.423 2316 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.55 % Allowed : 15.12 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.20), residues: 1872 helix: 2.97 (0.15), residues: 1108 sheet: 0.57 (0.40), residues: 200 loop : -1.57 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 338 TYR 0.014 0.001 TYR A 436 PHE 0.013 0.001 PHE B 182 TRP 0.007 0.001 TRP A 398 HIS 0.005 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00265 (15860) covalent geometry : angle 0.57934 (21496) SS BOND : bond 0.01380 ( 8) SS BOND : angle 3.38987 ( 16) hydrogen bonds : bond 0.05085 ( 996) hydrogen bonds : angle 4.04350 ( 3132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5076.19 seconds wall clock time: 87 minutes 10.00 seconds (5230.00 seconds total)