Starting phenix.real_space_refine on Fri Jul 3 19:03:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mgl_23828/07_2026/7mgl_23828.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mgl_23828/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mgl_23828/07_2026/7mgl_23828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mgl_23828/07_2026/7mgl_23828.map" model { file = "/net/cci-nas-00/data/ceres_data/7mgl_23828/07_2026/7mgl_23828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mgl_23828/07_2026/7mgl_23828.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mgl_23828/07_2026/7mgl_23828.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mgl_23828/07_2026/7mgl_23828.cif" } 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-6108/lib/python3.11/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: 3.32, per 1000 atoms: 0.21 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: 1.11 Conformation dependent library (CDL) restraints added in 663.9 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: 0.42 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: 2.81 Time building geometry restraints manager: 1.55 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 - 15.43: 7975 15.43 - 30.86: 940 30.86 - 46.29: 249 46.29 - 61.72: 76 61.72 - 77.15: 16 Dihedral angle restraints: 9256 sinusoidal: 3728 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 9253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2111 0.064 - 0.128: 304 0.128 - 0.191: 13 0.191 - 0.255: 0 0.255 - 0.319: 4 Chirality restraints: 2432 Sorted by residual: chirality pdb=" C07 ZB4 C 900 " pdb=" C08 ZB4 C 900 " pdb=" C12 ZB4 C 900 " pdb=" N01 ZB4 C 900 " both_signs ideal model delta sigma weight residual False -2.52 -2.84 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C07 ZB4 A 601 " pdb=" C08 ZB4 A 601 " pdb=" C12 ZB4 A 601 " pdb=" N01 ZB4 A 601 " both_signs ideal model delta sigma weight residual False -2.52 -2.84 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C07 ZB4 B 601 " pdb=" C08 ZB4 B 601 " pdb=" C12 ZB4 B 601 " pdb=" N01 ZB4 B 601 " both_signs ideal model delta sigma weight residual False -2.52 -2.84 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 2429 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 62 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO C 63 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 63 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 63 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 62 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO B 63 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 63 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 63 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 62 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO D 63 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 63 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 63 " -0.029 5.00e-02 4.00e+02 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 637 2.72 - 3.27: 15232 3.27 - 3.81: 24754 3.81 - 4.36: 30356 4.36 - 4.90: 52229 Nonbonded interactions: 123208 Sorted by model distance: nonbonded pdb=" NH2 ARG C 455 " pdb=" OE2 GLU D 95 " model vdw 2.177 3.120 nonbonded pdb=" OD1 ASP D 134 " pdb=" OH TYR D 218 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASP A 134 " pdb=" OH TYR A 218 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASP C 134 " pdb=" OH TYR C 218 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASP B 134 " pdb=" OH TYR B 218 " model vdw 2.261 3.040 ... (remaining 123203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 601) selection = (chain 'B' and resid 40 through 601) selection = chain 'C' selection = (chain 'D' and resid 40 through 601) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.240 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 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 : 14.841 77.150 5672 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/Z covalent geometry : bond 0.01290 / 0.64 (15860) covalent geometry : angle 0.83748 / 0.42 (21496) SS BOND : bond 0.00343 / 0.17 ( 8) SS BOND : angle 2.62542 / 1.52 ( 16) hydrogen bonds : bond 0.10096 / 6.60 ( 996) hydrogen bonds : angle 5.62223 / 4.03 ( 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 : 0.575 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: 0.4986 time to fit residues: 135.3490 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 : 0.491 ------------------------------------------------------------------------------- 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... 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 = 0.3828 r_free = 0.3828 target = 0.169411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.124868 restraints weight = 15942.450| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.87 r_work: 0.3071 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15868 Z= 0.140 Angle : 0.576 8.558 21512 Z= 0.302 Chirality : 0.041 0.133 2432 Planarity : 0.004 0.048 2640 Dihedral : 8.010 59.885 2226 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.20 % Allowed : 10.30 % Favored : 87.50 % 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: 0.64 (0.20), residues: 1872 helix: 1.85 (0.15), residues: 1108 sheet: -0.35 (0.39), residues: 196 loop : -2.28 (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 D 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/Z covalent geometry : bond 0.00295 / 0.14 (15860) covalent geometry : angle 0.57442 / 0.30 (21496) SS BOND : bond 0.00688 / 0.36 ( 8) SS BOND : angle 1.54133 / 0.79 ( 16) hydrogen bonds : bond 0.05770 / 3.89 ( 996) hydrogen bonds : angle 4.31778 / 3.10 ( 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 196 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.6615 (ptt) cc_final: 0.6067 (mtt) REVERT: A 174 HIS cc_start: 0.7442 (m170) cc_final: 0.6068 (t-90) REVERT: A 222 THR cc_start: 0.8891 (m) cc_final: 0.8648 (m) REVERT: A 283 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6737 (mm-30) REVERT: A 371 MET cc_start: 0.7753 (mtp) cc_final: 0.7476 (mtt) REVERT: B 168 ARG cc_start: 0.6755 (mtm110) cc_final: 0.6082 (mtt180) REVERT: B 283 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6914 (pm20) REVERT: B 322 ARG cc_start: 0.6441 (ttp-170) cc_final: 0.6116 (ttp-110) REVERT: B 371 MET cc_start: 0.7848 (mtp) cc_final: 0.7644 (mtt) REVERT: C 168 ARG cc_start: 0.6677 (mtm110) cc_final: 0.6010 (mtt180) REVERT: C 322 ARG cc_start: 0.6428 (ttp-170) cc_final: 0.6178 (ttp-110) REVERT: D 168 ARG cc_start: 0.6845 (mtm110) cc_final: 0.6101 (mtt180) REVERT: D 176 ASP cc_start: 0.7140 (t0) cc_final: 0.6668 (t70) REVERT: D 276 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: D 322 ARG cc_start: 0.6218 (ttp-170) cc_final: 0.5883 (ttp-110) REVERT: D 467 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8684 (mt) outliers start: 37 outliers final: 13 residues processed: 187 average time/residue: 0.4245 time to fit residues: 90.2723 Evaluate side-chains 153 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 A residue 456 SER Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 452 VAL 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: 2.9990 chunk 148 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 170 optimal weight: 0.4980 chunk 135 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 HIS ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 495 GLN C 267 HIS C 286 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS D 97 ASN D 286 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.162177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.115743 restraints weight = 16273.480| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.88 r_work: 0.2963 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15868 Z= 0.164 Angle : 0.590 7.745 21512 Z= 0.307 Chirality : 0.042 0.186 2432 Planarity : 0.004 0.042 2640 Dihedral : 7.415 59.443 2205 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.80 % Allowed : 11.85 % Favored : 85.36 % 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: 1.24 (0.20), residues: 1872 helix: 2.29 (0.15), residues: 1108 sheet: -0.04 (0.37), residues: 204 loop : -1.98 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.018 0.002 TYR C 436 PHE 0.014 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/Z covalent geometry : bond 0.00368 / 0.16 (15860) covalent geometry : angle 0.58603 / 0.31 (21496) SS BOND : bond 0.01141 / 0.64 ( 8) SS BOND : angle 2.56541 / 1.35 ( 16) hydrogen bonds : bond 0.06336 / 4.26 ( 996) hydrogen bonds : angle 4.31708 / 3.09 ( 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 201 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.6824 (ptt) cc_final: 0.6353 (mtt) REVERT: A 115 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6644 (p0) REVERT: A 174 HIS cc_start: 0.7426 (m170) cc_final: 0.5654 (t-90) REVERT: A 283 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6940 (pm20) REVERT: A 371 MET cc_start: 0.7825 (mtp) cc_final: 0.7590 (mtt) REVERT: B 115 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.6730 (p0) REVERT: B 168 ARG cc_start: 0.6934 (mtm110) cc_final: 0.6073 (mtt180) REVERT: B 283 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6868 (pm20) REVERT: B 322 ARG cc_start: 0.6355 (ttp-170) cc_final: 0.6058 (ttp-110) REVERT: B 371 MET cc_start: 0.7913 (mtp) cc_final: 0.7684 (mtt) REVERT: B 376 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6755 (mm-30) REVERT: C 115 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6604 (p0) REVERT: C 168 ARG cc_start: 0.6893 (mtm110) cc_final: 0.6089 (mtt180) REVERT: C 322 ARG cc_start: 0.6400 (ttp-170) cc_final: 0.6094 (ttp-110) REVERT: D 115 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6673 (p0) REVERT: D 168 ARG cc_start: 0.7000 (mtm110) cc_final: 0.6137 (mtt180) REVERT: D 176 ASP cc_start: 0.7095 (t0) cc_final: 0.6558 (t70) REVERT: D 322 ARG cc_start: 0.6199 (ttp-170) cc_final: 0.5899 (ttp-110) REVERT: D 467 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8739 (mt) outliers start: 47 outliers final: 22 residues processed: 195 average time/residue: 0.4141 time to fit residues: 92.2512 Evaluate side-chains 167 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 239 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 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 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 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: 1.9990 chunk 140 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN A 267 HIS ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 495 GLN 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 C 495 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS D 495 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.156710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.109130 restraints weight = 16372.789| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.95 r_work: 0.2916 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15868 Z= 0.257 Angle : 0.696 11.786 21512 Z= 0.356 Chirality : 0.046 0.206 2432 Planarity : 0.005 0.042 2640 Dihedral : 7.445 53.308 2205 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.93 % Allowed : 11.79 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.15 (0.20), residues: 1872 helix: 2.18 (0.15), residues: 1108 sheet: -0.08 (0.37), residues: 204 loop : -1.95 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 455 TYR 0.020 0.002 TYR D 436 PHE 0.017 0.002 PHE A 182 TRP 0.007 0.001 TRP A 491 HIS 0.009 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.26 (15860) covalent geometry : angle 0.68898 / 0.35 (21496) SS BOND : bond 0.01888 / 1.08 ( 8) SS BOND : angle 3.61352 / 1.87 ( 16) hydrogen bonds : bond 0.07669 / 5.16 ( 996) hydrogen bonds : angle 4.53482 / 3.24 ( 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 201 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 135 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.6986 (ptt) cc_final: 0.6474 (mtt) REVERT: A 89 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7990 (tm) REVERT: A 146 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7505 (tpp80) REVERT: A 174 HIS cc_start: 0.7308 (m170) cc_final: 0.5400 (t-90) REVERT: A 283 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6936 (pm20) REVERT: A 371 MET cc_start: 0.7957 (mtp) cc_final: 0.7709 (mtt) REVERT: B 89 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7978 (tm) REVERT: B 115 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6640 (p0) REVERT: B 168 ARG cc_start: 0.6976 (mtm110) cc_final: 0.6071 (mtt180) REVERT: B 196 ASP cc_start: 0.7685 (t70) cc_final: 0.7374 (t0) REVERT: B 276 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: B 283 GLU cc_start: 0.7433 (mm-30) cc_final: 0.6902 (pm20) REVERT: B 322 ARG cc_start: 0.6451 (ttp-170) cc_final: 0.6121 (ttp-110) REVERT: C 89 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7962 (tm) REVERT: C 115 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6598 (p0) REVERT: C 168 ARG cc_start: 0.6988 (mtm110) cc_final: 0.6086 (mtt180) REVERT: C 196 ASP cc_start: 0.7621 (t70) cc_final: 0.7356 (t0) REVERT: C 276 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: C 322 ARG cc_start: 0.6522 (ttp-170) cc_final: 0.6191 (ttp-110) REVERT: D 89 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7940 (tm) REVERT: D 115 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6644 (p0) REVERT: D 168 ARG cc_start: 0.7004 (mtm110) cc_final: 0.6090 (mtt180) REVERT: D 176 ASP cc_start: 0.7167 (t0) cc_final: 0.6560 (t70) REVERT: D 276 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: D 322 ARG cc_start: 0.6342 (ttp-170) cc_final: 0.6052 (ttp-110) REVERT: D 467 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8728 (mt) outliers start: 66 outliers final: 27 residues processed: 192 average time/residue: 0.4222 time to fit residues: 91.7411 Evaluate side-chains 169 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 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 363 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 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: 0.0270 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 90 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 HIS A 451 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS C 131 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.167948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.125121 restraints weight = 16126.864| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.76 r_work: 0.3114 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15868 Z= 0.121 Angle : 0.555 13.256 21512 Z= 0.285 Chirality : 0.040 0.200 2432 Planarity : 0.004 0.043 2640 Dihedral : 6.892 59.919 2204 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.96 % Allowed : 14.05 % Favored : 83.99 % 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: 1.69 (0.20), residues: 1872 helix: 2.60 (0.15), residues: 1108 sheet: 0.09 (0.38), residues: 196 loop : -1.64 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 347 TYR 0.012 0.001 TYR A 497 PHE 0.010 0.001 PHE A 182 TRP 0.007 0.001 TRP B 398 HIS 0.006 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (15860) covalent geometry : angle 0.54347 / 0.28 (21496) SS BOND : bond 0.01370 / 0.76 ( 8) SS BOND : angle 4.08571 / 2.28 ( 16) hydrogen bonds : bond 0.04978 / 3.34 ( 996) hydrogen bonds : angle 4.01825 / 2.88 ( 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 181 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.6683 (ptt) cc_final: 0.6283 (mtt) REVERT: A 174 HIS cc_start: 0.7315 (m170) cc_final: 0.5602 (t70) REVERT: A 283 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6913 (pm20) REVERT: A 322 ARG cc_start: 0.6556 (ttp-170) cc_final: 0.6337 (ttp-110) REVERT: B 89 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7786 (tm) REVERT: B 168 ARG cc_start: 0.6866 (mtm110) cc_final: 0.6111 (mmt90) REVERT: B 196 ASP cc_start: 0.7602 (t70) cc_final: 0.7363 (t0) REVERT: B 283 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6824 (pm20) REVERT: B 322 ARG cc_start: 0.6400 (ttp-170) cc_final: 0.6029 (ttp-110) REVERT: C 168 ARG cc_start: 0.6874 (mtm110) cc_final: 0.6107 (mpt180) REVERT: C 322 ARG cc_start: 0.6370 (ttp-170) cc_final: 0.5981 (ttp-110) REVERT: D 168 ARG cc_start: 0.6884 (mtm110) cc_final: 0.6130 (mmt90) REVERT: D 176 ASP cc_start: 0.7169 (t0) cc_final: 0.6657 (t70) REVERT: D 322 ARG cc_start: 0.6299 (ttp-170) cc_final: 0.5965 (ttp-110) outliers start: 33 outliers final: 13 residues processed: 175 average time/residue: 0.4296 time to fit residues: 85.2957 Evaluate side-chains 153 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 239 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 239 THR 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: 0.9980 chunk 35 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 HIS B 451 HIS C 451 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.160383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.116196 restraints weight = 16229.833| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.79 r_work: 0.2980 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2329 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= 0.204 Angle : 0.700 14.040 21512 Z= 0.354 Chirality : 0.045 0.275 2432 Planarity : 0.004 0.041 2640 Dihedral : 7.226 56.062 2204 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.90 % Allowed : 14.64 % Favored : 83.45 % 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: 2.54 (0.15), residues: 1108 sheet: -0.20 (0.38), residues: 200 loop : -1.72 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 455 TYR 0.020 0.002 TYR A 436 PHE 0.016 0.001 PHE B 182 TRP 0.005 0.001 TRP C 491 HIS 0.008 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 (15860) covalent geometry : angle 0.67472 / 0.34 (21496) SS BOND : bond 0.01675 / 0.96 ( 8) SS BOND : angle 6.80643 / 3.70 ( 16) hydrogen bonds : bond 0.06879 / 4.63 ( 996) hydrogen bonds : angle 4.34809 / 3.11 ( 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 170 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6864 (ptt) cc_final: 0.6484 (mtt) REVERT: A 89 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7825 (tm) REVERT: B 89 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7832 (tm) REVERT: B 168 ARG cc_start: 0.6874 (mtm110) cc_final: 0.5931 (mtt180) REVERT: B 285 LYS cc_start: 0.6156 (mptt) cc_final: 0.5732 (mptt) REVERT: B 322 ARG cc_start: 0.6298 (ttp-170) cc_final: 0.5911 (ttp-110) REVERT: C 89 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7827 (tm) REVERT: C 168 ARG cc_start: 0.6879 (mtm110) cc_final: 0.5953 (mtt180) REVERT: C 285 LYS cc_start: 0.6059 (mptt) cc_final: 0.5507 (mptt) REVERT: C 322 ARG cc_start: 0.6268 (ttp-170) cc_final: 0.5958 (ttp-110) REVERT: D 89 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7818 (tm) REVERT: D 168 ARG cc_start: 0.6854 (mtm110) cc_final: 0.5925 (mtt180) REVERT: D 285 LYS cc_start: 0.6259 (mptt) cc_final: 0.5703 (mptt) REVERT: D 322 ARG cc_start: 0.6226 (ttp-170) cc_final: 0.5887 (ttp-110) outliers start: 32 outliers final: 19 residues processed: 163 average time/residue: 0.4620 time to fit residues: 85.0905 Evaluate side-chains 160 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 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 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 8 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 HIS B 451 HIS C 451 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.159407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.111778 restraints weight = 16125.874| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.95 r_work: 0.2922 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15868 Z= 0.201 Angle : 0.686 14.344 21512 Z= 0.348 Chirality : 0.045 0.302 2432 Planarity : 0.004 0.042 2640 Dihedral : 7.192 58.042 2204 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.66 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: 1.49 (0.20), residues: 1872 helix: 2.49 (0.15), residues: 1108 sheet: -0.14 (0.38), residues: 200 loop : -1.79 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 455 TYR 0.018 0.002 TYR A 436 PHE 0.016 0.001 PHE B 182 TRP 0.008 0.001 TRP C 444 HIS 0.009 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (15860) covalent geometry : angle 0.66915 / 0.34 (21496) SS BOND : bond 0.01660 / 0.96 ( 8) SS BOND : angle 5.52760 / 3.03 ( 16) hydrogen bonds : bond 0.06840 / 4.61 ( 996) hydrogen bonds : angle 4.36597 / 3.12 ( 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 181 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6963 (ptt) cc_final: 0.6608 (mtt) REVERT: A 89 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7863 (tm) REVERT: B 89 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7905 (tm) REVERT: B 168 ARG cc_start: 0.6951 (mtm110) cc_final: 0.6010 (mtt180) REVERT: B 285 LYS cc_start: 0.6369 (mptt) cc_final: 0.5909 (mptt) REVERT: C 89 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7907 (tm) REVERT: C 168 ARG cc_start: 0.6977 (mtm110) cc_final: 0.6019 (mtt180) REVERT: C 276 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: C 285 LYS cc_start: 0.6249 (mptt) cc_final: 0.5758 (mptt) REVERT: C 322 ARG cc_start: 0.6350 (ttp-170) cc_final: 0.6048 (ttp-110) REVERT: D 89 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7886 (tm) REVERT: D 168 ARG cc_start: 0.6950 (mtm110) cc_final: 0.5993 (mtt180) REVERT: D 276 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: D 285 LYS cc_start: 0.6200 (mptt) cc_final: 0.5705 (mptt) REVERT: D 322 ARG cc_start: 0.6261 (ttp-170) cc_final: 0.5862 (ttp-110) REVERT: D 467 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8753 (mt) outliers start: 41 outliers final: 22 residues processed: 168 average time/residue: 0.4170 time to fit residues: 79.1166 Evaluate side-chains 163 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 174 HIS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 89 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 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.0655 > 50: distance: 2 - 15: 3.018 distance: 78 - 193: 17.725 distance: 81 - 190: 21.642 distance: 129 - 201: 12.519 distance: 131 - 137: 15.541 distance: 137 - 138: 14.606 distance: 138 - 139: 9.033 distance: 138 - 141: 25.508 distance: 139 - 140: 17.609 distance: 139 - 145: 19.813 distance: 141 - 142: 21.278 distance: 142 - 143: 4.281 distance: 142 - 144: 15.767 distance: 145 - 146: 11.338 distance: 146 - 147: 5.749 distance: 146 - 149: 14.107 distance: 147 - 148: 19.843 distance: 147 - 154: 24.784 distance: 149 - 150: 29.111 distance: 150 - 151: 12.952 distance: 151 - 152: 32.247 distance: 152 - 153: 11.998 distance: 154 - 155: 16.089 distance: 155 - 156: 9.833 distance: 156 - 157: 7.739 distance: 156 - 159: 64.753 distance: 159 - 160: 38.847 distance: 160 - 161: 27.404 distance: 160 - 163: 28.495 distance: 161 - 162: 8.736 distance: 163 - 164: 16.835 distance: 164 - 165: 13.736 distance: 164 - 166: 25.344 distance: 165 - 167: 27.205 distance: 166 - 168: 12.249 distance: 167 - 168: 38.644 distance: 170 - 171: 23.479 distance: 170 - 173: 17.005 distance: 171 - 172: 15.658 distance: 171 - 175: 7.293 distance: 173 - 174: 16.317 distance: 175 - 176: 24.433 distance: 176 - 177: 23.528 distance: 177 - 178: 21.822 distance: 177 - 179: 47.976 distance: 179 - 180: 10.322 distance: 180 - 181: 9.054 distance: 180 - 183: 25.126 distance: 181 - 182: 12.692 distance: 181 - 190: 36.073 distance: 183 - 184: 27.553 distance: 184 - 185: 26.368 distance: 185 - 186: 7.369 distance: 186 - 187: 7.298 distance: 187 - 188: 13.106 distance: 187 - 189: 13.010 distance: 190 - 191: 21.046 distance: 191 - 192: 16.306 distance: 191 - 194: 8.808 distance: 192 - 193: 13.189 distance: 192 - 198: 37.778 distance: 194 - 195: 16.120 distance: 194 - 196: 17.354 distance: 195 - 197: 27.426 distance: 198 - 199: 17.444 distance: 198 - 204: 10.017 distance: 199 - 200: 12.809 distance: 199 - 202: 15.558 distance: 200 - 201: 26.677 distance: 200 - 205: 17.924 distance: 202 - 203: 12.749 distance: 203 - 204: 19.903 distance: 205 - 206: 13.798 distance: 206 - 207: 6.266 distance: 206 - 209: 12.165 distance: 207 - 208: 19.661 distance: 207 - 213: 27.780 distance: 209 - 210: 38.516 distance: 209 - 211: 23.775 distance: 210 - 212: 18.467