Starting phenix.real_space_refine on Tue Nov 18 15:13:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sq8_25379/11_2025/7sq8_25379_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sq8_25379/11_2025/7sq8_25379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.598 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sq8_25379/11_2025/7sq8_25379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sq8_25379/11_2025/7sq8_25379.map" model { file = "/net/cci-nas-00/data/ceres_data/7sq8_25379/11_2025/7sq8_25379_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sq8_25379/11_2025/7sq8_25379_neut.cif" } resolution = 2.598 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= 0.007 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 S 96 5.16 5 Na 1 4.78 5 C 9904 2.51 5 N 2500 2.21 5 O 2616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15117 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3749 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 13, 'TRANS': 449} Chain breaks: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 3.45, per 1000 atoms: 0.23 Number of scatterers: 15117 At special positions: 0 Unit cell: (108.73, 108.73, 114.54, 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 96 16.00 Na 1 11.00 O 2616 8.00 N 2500 7.00 C 9904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 230 " " NAG F 1 " - " ASN B 230 " " NAG G 1 " - " ASN C 230 " " NAG H 1 " - " ASN D 230 " Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 565.5 milliseconds 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 66.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 51 through 58 removed outlier: 3.867A pdb=" N ARG A 57 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 106 removed outlier: 4.073A pdb=" N MET A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 138 Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 297 through 338 removed outlier: 3.523A pdb=" N TRP A 335 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 352 through 377 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.622A pdb=" N CYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.889A pdb=" N LEU A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 448 removed outlier: 4.030A pdb=" N LEU A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 3.997A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 4.064A pdb=" N ARG A 455 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 469 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.819A pdb=" N THR A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 508 Processing helix chain 'A' and resid 508 through 526 Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 51 through 58 removed outlier: 3.867A pdb=" N ARG B 57 " --> pdb=" O CYS B 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 106 removed outlier: 4.073A pdb=" N MET B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 138 Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 297 through 338 removed outlier: 3.523A pdb=" N TRP B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 349 Processing helix chain 'B' and resid 352 through 377 Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.622A pdb=" N CYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.889A pdb=" N LEU B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 448 removed outlier: 4.030A pdb=" N LEU B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 3.998A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 4.064A pdb=" N ARG B 455 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 469 Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.813A pdb=" N THR B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 508 Processing helix chain 'B' and resid 508 through 526 Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 51 through 58 removed outlier: 3.867A pdb=" N ARG C 57 " --> pdb=" O CYS C 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 58 " --> pdb=" O ASP C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 106 removed outlier: 4.073A pdb=" N MET C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 138 Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 297 through 338 removed outlier: 3.523A pdb=" N TRP C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 349 Processing helix chain 'C' and resid 352 through 377 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.622A pdb=" N CYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.889A pdb=" N LEU C 405 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 448 removed outlier: 4.030A pdb=" N LEU C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 3.998A pdb=" N VAL C 434 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 removed outlier: 4.064A pdb=" N ARG C 455 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 469 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.837A pdb=" N THR C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 508 Processing helix chain 'C' and resid 508 through 526 Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 51 through 58 removed outlier: 3.867A pdb=" N ARG D 57 " --> pdb=" O CYS D 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 58 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 106 removed outlier: 4.072A pdb=" N MET D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 297 through 338 removed outlier: 3.523A pdb=" N TRP D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 349 Processing helix chain 'D' and resid 352 through 377 Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.622A pdb=" N CYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.889A pdb=" N LEU D 405 " --> pdb=" O VAL D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 448 removed outlier: 4.030A pdb=" N LEU D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 3.998A pdb=" N VAL D 434 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 removed outlier: 4.063A pdb=" N ARG D 455 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 469 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.814A pdb=" N THR D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 508 Processing helix chain 'D' and resid 508 through 526 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP A 252 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP A 252 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG A 168 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 231 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS A 166 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE A 233 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA A 164 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.596A pdb=" N ASP A 176 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP B 252 " --> pdb=" O ASN B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP B 252 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG B 168 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL B 231 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS B 166 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B 233 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA B 164 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.596A pdb=" N ASP B 176 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP C 252 " --> pdb=" O ASN C 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP C 252 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG C 168 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL C 231 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS C 166 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE C 233 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA C 164 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 175 through 176 removed outlier: 3.596A pdb=" N ASP C 176 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP D 252 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 118 through 119 removed outlier: 4.614A pdb=" N ASP D 252 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG D 168 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL D 231 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS D 166 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE D 233 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA D 164 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 175 through 176 removed outlier: 3.597A pdb=" N ASP D 176 " --> pdb=" O THR D 181 " (cutoff:3.500A) 1132 hydrogen bonds defined for protein. 3288 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: 2.79 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3190 1.33 - 1.45: 3635 1.45 - 1.57: 8511 1.57 - 1.69: 4 1.69 - 1.81: 132 Bond restraints: 15472 Sorted by residual: bond pdb=" CA ASP A 196 " pdb=" C ASP A 196 " ideal model delta sigma weight residual 1.523 1.574 -0.051 1.06e-02 8.90e+03 2.32e+01 bond pdb=" CA ASP D 196 " pdb=" C ASP D 196 " ideal model delta sigma weight residual 1.523 1.574 -0.051 1.06e-02 8.90e+03 2.31e+01 bond pdb=" CA ASP B 196 " pdb=" C ASP B 196 " ideal model delta sigma weight residual 1.523 1.573 -0.051 1.06e-02 8.90e+03 2.28e+01 bond pdb=" CA ASP C 196 " pdb=" C ASP C 196 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.06e-02 8.90e+03 2.26e+01 bond pdb=" C ASP C 196 " pdb=" N PRO C 197 " ideal model delta sigma weight residual 1.335 1.377 -0.043 1.15e-02 7.56e+03 1.37e+01 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 20177 1.29 - 2.57: 653 2.57 - 3.86: 126 3.86 - 5.14: 20 5.14 - 6.43: 4 Bond angle restraints: 20980 Sorted by residual: angle pdb=" C ALA B 58 " pdb=" N LYS B 59 " pdb=" CA LYS B 59 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C ALA C 58 " pdb=" N LYS C 59 " pdb=" CA LYS C 59 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C ALA A 58 " pdb=" N LYS A 59 " pdb=" CA LYS A 59 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C ALA D 58 " pdb=" N LYS D 59 " pdb=" CA LYS D 59 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" N ALA C 482 " pdb=" CA ALA C 482 " pdb=" C ALA C 482 " ideal model delta sigma weight residual 110.97 114.61 -3.64 1.09e+00 8.42e-01 1.12e+01 ... (remaining 20975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 8320 17.30 - 34.59: 689 34.59 - 51.89: 120 51.89 - 69.18: 11 69.18 - 86.48: 20 Dihedral angle restraints: 9160 sinusoidal: 3724 harmonic: 5436 Sorted by residual: dihedral pdb=" CG ARG D 419 " pdb=" CD ARG D 419 " pdb=" NE ARG D 419 " pdb=" CZ ARG D 419 " ideal model delta sinusoidal sigma weight residual -90.00 -131.89 41.89 2 1.50e+01 4.44e-03 9.51e+00 dihedral pdb=" CG ARG C 419 " pdb=" CD ARG C 419 " pdb=" NE ARG C 419 " pdb=" CZ ARG C 419 " ideal model delta sinusoidal sigma weight residual -90.00 -131.84 41.84 2 1.50e+01 4.44e-03 9.49e+00 dihedral pdb=" CG ARG B 419 " pdb=" CD ARG B 419 " pdb=" NE ARG B 419 " pdb=" CZ ARG B 419 " ideal model delta sinusoidal sigma weight residual -90.00 -131.80 41.80 2 1.50e+01 4.44e-03 9.48e+00 ... (remaining 9157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1991 0.052 - 0.104: 367 0.104 - 0.156: 66 0.156 - 0.208: 0 0.208 - 0.260: 12 Chirality restraints: 2436 Sorted by residual: chirality pdb=" CA HIS D 486 " pdb=" N HIS D 486 " pdb=" C HIS D 486 " pdb=" CB HIS D 486 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA HIS C 486 " pdb=" N HIS C 486 " pdb=" C HIS C 486 " pdb=" CB HIS C 486 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA HIS A 486 " pdb=" N HIS A 486 " pdb=" C HIS A 486 " pdb=" CB HIS A 486 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2433 not shown) Planarity restraints: 2572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 471 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" C ASP D 471 " 0.024 2.00e-02 2.50e+03 pdb=" O ASP D 471 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP D 472 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 471 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C ASP B 471 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP B 471 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP B 472 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 471 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" C ASP C 471 " 0.022 2.00e-02 2.50e+03 pdb=" O ASP C 471 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP C 472 " -0.007 2.00e-02 2.50e+03 ... (remaining 2569 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 994 2.74 - 3.28: 15338 3.28 - 3.82: 25994 3.82 - 4.36: 30876 4.36 - 4.90: 52933 Nonbonded interactions: 126135 Sorted by model distance: nonbonded pdb=" OD1 ASP C 134 " pdb=" OH TYR C 218 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP D 134 " pdb=" OH TYR D 218 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP A 134 " pdb=" OH TYR A 218 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP B 134 " pdb=" OH TYR B 218 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP A 384 " pdb=" OH TYR B 450 " model vdw 2.243 3.040 ... (remaining 126130 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' selection = chain 'B' selection = (chain 'C' and resid 40 through 527) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.520 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.004 0.051 15480 Z= 0.194 Angle : 0.559 6.426 21004 Z= 0.326 Chirality : 0.044 0.260 2436 Planarity : 0.003 0.028 2568 Dihedral : 13.318 86.476 5656 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 1.93 (0.20), residues: 1828 helix: 2.07 (0.16), residues: 1140 sheet: 1.05 (0.34), residues: 252 loop : -0.70 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 419 TYR 0.015 0.001 TYR C 497 PHE 0.011 0.001 PHE A 505 TRP 0.011 0.002 TRP C 398 HIS 0.003 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00351 (15472) covalent geometry : angle 0.55397 (20980) hydrogen bonds : bond 0.12909 ( 1036) hydrogen bonds : angle 6.50918 ( 3288) link_BETA1-4 : bond 0.00204 ( 4) link_BETA1-4 : angle 2.69937 ( 12) link_NAG-ASN : bond 0.00108 ( 4) link_NAG-ASN : angle 1.64545 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.574 Fit side-chains REVERT: A 322 ARG cc_start: 0.6572 (mtp-110) cc_final: 0.6359 (ttm170) REVERT: A 324 PHE cc_start: 0.6479 (t80) cc_final: 0.6165 (t80) REVERT: B 322 ARG cc_start: 0.6555 (mtp-110) cc_final: 0.6333 (ttm170) REVERT: B 324 PHE cc_start: 0.6414 (t80) cc_final: 0.6098 (t80) REVERT: C 322 ARG cc_start: 0.6553 (mtp-110) cc_final: 0.6337 (ttm170) REVERT: C 324 PHE cc_start: 0.6428 (t80) cc_final: 0.6101 (t80) REVERT: D 324 PHE cc_start: 0.6446 (t80) cc_final: 0.6118 (t80) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.5379 time to fit residues: 113.3726 Evaluate side-chains 129 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 226 HIS A 352 ASN A 483 GLN B 194 GLN B 226 HIS B 352 ASN B 483 GLN C 194 GLN C 226 HIS C 352 ASN C 483 GLN D 194 GLN D 226 HIS D 352 ASN D 483 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.142905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.102009 restraints weight = 16225.255| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.62 r_work: 0.2809 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15480 Z= 0.199 Angle : 0.588 4.786 21004 Z= 0.318 Chirality : 0.044 0.142 2436 Planarity : 0.004 0.033 2568 Dihedral : 4.905 33.787 2208 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.36 % Allowed : 5.68 % Favored : 91.97 % 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: 2.06 (0.19), residues: 1828 helix: 2.21 (0.15), residues: 1100 sheet: 1.04 (0.34), residues: 252 loop : -0.45 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 337 TYR 0.016 0.002 TYR D 497 PHE 0.017 0.002 PHE B 474 TRP 0.014 0.002 TRP B 398 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00462 (15472) covalent geometry : angle 0.58361 (20980) hydrogen bonds : bond 0.06161 ( 1036) hydrogen bonds : angle 5.03262 ( 3288) link_BETA1-4 : bond 0.00184 ( 4) link_BETA1-4 : angle 2.29960 ( 12) link_NAG-ASN : bond 0.00361 ( 4) link_NAG-ASN : angle 2.00652 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.589 Fit side-chains REVERT: A 322 ARG cc_start: 0.6925 (mtp-110) cc_final: 0.6466 (ttm170) REVERT: A 324 PHE cc_start: 0.6255 (t80) cc_final: 0.5939 (t80) REVERT: A 483 GLN cc_start: 0.6113 (OUTLIER) cc_final: 0.4544 (mm110) REVERT: B 322 ARG cc_start: 0.6926 (mtp-110) cc_final: 0.6457 (ttm170) REVERT: B 324 PHE cc_start: 0.6220 (t80) cc_final: 0.5912 (t80) REVERT: B 483 GLN cc_start: 0.6107 (OUTLIER) cc_final: 0.4548 (mm110) REVERT: C 322 ARG cc_start: 0.6887 (mtp-110) cc_final: 0.6473 (ttm110) REVERT: C 324 PHE cc_start: 0.6231 (t80) cc_final: 0.5901 (t80) REVERT: C 483 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.4555 (mm110) REVERT: D 324 PHE cc_start: 0.6260 (t80) cc_final: 0.5908 (t80) REVERT: D 483 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.4548 (mm110) outliers start: 39 outliers final: 16 residues processed: 159 average time/residue: 0.5426 time to fit residues: 96.2473 Evaluate side-chains 144 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 483 GLN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 483 GLN Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 469 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.102662 restraints weight = 16338.924| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.72 r_work: 0.2831 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15480 Z= 0.126 Angle : 0.492 4.753 21004 Z= 0.270 Chirality : 0.040 0.126 2436 Planarity : 0.003 0.033 2568 Dihedral : 4.460 30.103 2208 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.99 % Allowed : 7.13 % Favored : 90.88 % 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: 2.33 (0.19), residues: 1828 helix: 2.36 (0.15), residues: 1120 sheet: 1.25 (0.35), residues: 252 loop : -0.36 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 200 TYR 0.014 0.001 TYR C 497 PHE 0.015 0.001 PHE B 350 TRP 0.010 0.001 TRP C 398 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00259 (15472) covalent geometry : angle 0.48892 (20980) hydrogen bonds : bond 0.05124 ( 1036) hydrogen bonds : angle 4.64916 ( 3288) link_BETA1-4 : bond 0.00067 ( 4) link_BETA1-4 : angle 2.10860 ( 12) link_NAG-ASN : bond 0.00064 ( 4) link_NAG-ASN : angle 1.12668 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.566 Fit side-chains REVERT: A 322 ARG cc_start: 0.6911 (mtp-110) cc_final: 0.6503 (ttm110) REVERT: A 324 PHE cc_start: 0.6208 (t80) cc_final: 0.5921 (t80) REVERT: A 371 MET cc_start: 0.8230 (mtp) cc_final: 0.7833 (mtm) REVERT: B 322 ARG cc_start: 0.6890 (mtp-110) cc_final: 0.6474 (ttm110) REVERT: B 324 PHE cc_start: 0.6185 (t80) cc_final: 0.5898 (t80) REVERT: C 322 ARG cc_start: 0.6868 (mtp-110) cc_final: 0.6466 (ttm110) REVERT: C 324 PHE cc_start: 0.6186 (t80) cc_final: 0.5901 (t80) REVERT: D 324 PHE cc_start: 0.6221 (t80) cc_final: 0.5893 (t80) REVERT: D 371 MET cc_start: 0.8202 (mtp) cc_final: 0.7803 (mtm) outliers start: 33 outliers final: 16 residues processed: 145 average time/residue: 0.5125 time to fit residues: 83.5252 Evaluate side-chains 127 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 10 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.144198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.102823 restraints weight = 16196.878| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.74 r_work: 0.2813 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15480 Z= 0.177 Angle : 0.552 5.887 21004 Z= 0.299 Chirality : 0.042 0.138 2436 Planarity : 0.004 0.032 2568 Dihedral : 4.766 31.788 2208 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.48 % Allowed : 8.27 % Favored : 89.25 % 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: 2.22 (0.19), residues: 1828 helix: 2.29 (0.15), residues: 1116 sheet: 1.27 (0.34), residues: 252 loop : -0.48 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 200 TYR 0.016 0.002 TYR B 497 PHE 0.017 0.002 PHE D 350 TRP 0.013 0.002 TRP C 398 HIS 0.004 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00405 (15472) covalent geometry : angle 0.54760 (20980) hydrogen bonds : bond 0.05830 ( 1036) hydrogen bonds : angle 4.74760 ( 3288) link_BETA1-4 : bond 0.00013 ( 4) link_BETA1-4 : angle 2.34637 ( 12) link_NAG-ASN : bond 0.00199 ( 4) link_NAG-ASN : angle 1.84746 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.630 Fit side-chains REVERT: A 175 VAL cc_start: 0.7380 (t) cc_final: 0.7172 (t) REVERT: A 322 ARG cc_start: 0.6946 (mtp-110) cc_final: 0.6515 (ttm110) REVERT: A 324 PHE cc_start: 0.6218 (t80) cc_final: 0.5964 (t80) REVERT: B 322 ARG cc_start: 0.6946 (mtp-110) cc_final: 0.6490 (ttm110) REVERT: B 324 PHE cc_start: 0.6207 (t80) cc_final: 0.5942 (t80) REVERT: C 322 ARG cc_start: 0.6898 (mtp-110) cc_final: 0.6458 (ttm110) REVERT: C 324 PHE cc_start: 0.6173 (t80) cc_final: 0.5906 (t80) outliers start: 41 outliers final: 18 residues processed: 157 average time/residue: 0.5442 time to fit residues: 95.3055 Evaluate side-chains 144 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 127 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 94 optimal weight: 0.0470 chunk 124 optimal weight: 3.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 ASN A 483 GLN B 469 ASN B 483 GLN C 483 GLN D 469 ASN D 483 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.147671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.107074 restraints weight = 16314.489| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.70 r_work: 0.2869 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15480 Z= 0.113 Angle : 0.474 5.899 21004 Z= 0.258 Chirality : 0.039 0.127 2436 Planarity : 0.003 0.037 2568 Dihedral : 4.258 27.268 2208 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.75 % Allowed : 9.42 % Favored : 88.83 % 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: 2.30 (0.19), residues: 1828 helix: 2.36 (0.15), residues: 1140 sheet: 1.42 (0.35), residues: 252 loop : -0.75 (0.25), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 200 TYR 0.014 0.001 TYR D 497 PHE 0.013 0.001 PHE C 350 TRP 0.008 0.001 TRP C 398 HIS 0.003 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00227 (15472) covalent geometry : angle 0.47106 (20980) hydrogen bonds : bond 0.04722 ( 1036) hydrogen bonds : angle 4.39450 ( 3288) link_BETA1-4 : bond 0.00106 ( 4) link_BETA1-4 : angle 2.18733 ( 12) link_NAG-ASN : bond 0.00029 ( 4) link_NAG-ASN : angle 0.77924 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.553 Fit side-chains REVERT: A 176 ASP cc_start: 0.6712 (t0) cc_final: 0.6384 (t0) REVERT: A 322 ARG cc_start: 0.6892 (mtp-110) cc_final: 0.6427 (ttm110) REVERT: A 324 PHE cc_start: 0.6182 (t80) cc_final: 0.5927 (t80) REVERT: B 176 ASP cc_start: 0.6821 (t0) cc_final: 0.6477 (t0) REVERT: B 322 ARG cc_start: 0.6832 (mtp-110) cc_final: 0.6376 (ttm110) REVERT: B 324 PHE cc_start: 0.6164 (t80) cc_final: 0.5914 (t80) REVERT: C 176 ASP cc_start: 0.6742 (t0) cc_final: 0.6488 (t0) REVERT: C 322 ARG cc_start: 0.6830 (mtp-110) cc_final: 0.6371 (ttm110) REVERT: C 324 PHE cc_start: 0.6198 (t80) cc_final: 0.5938 (t80) REVERT: D 176 ASP cc_start: 0.6726 (t0) cc_final: 0.6468 (t0) REVERT: D 324 PHE cc_start: 0.6230 (t80) cc_final: 0.5948 (t80) outliers start: 29 outliers final: 9 residues processed: 141 average time/residue: 0.5711 time to fit residues: 89.3264 Evaluate side-chains 130 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 146 optimal weight: 0.0770 chunk 180 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 overall best weight: 2.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS B 226 HIS C 226 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.144554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.103686 restraints weight = 16190.499| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.74 r_work: 0.2813 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15480 Z= 0.179 Angle : 0.558 6.372 21004 Z= 0.300 Chirality : 0.043 0.135 2436 Planarity : 0.004 0.034 2568 Dihedral : 4.727 30.382 2208 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.20 % Allowed : 8.64 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.31 (0.19), residues: 1828 helix: 2.36 (0.15), residues: 1116 sheet: 1.37 (0.34), residues: 252 loop : -0.52 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 200 TYR 0.017 0.002 TYR C 497 PHE 0.016 0.002 PHE C 235 TRP 0.013 0.002 TRP C 398 HIS 0.004 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00413 (15472) covalent geometry : angle 0.55359 (20980) hydrogen bonds : bond 0.05826 ( 1036) hydrogen bonds : angle 4.67690 ( 3288) link_BETA1-4 : bond 0.00024 ( 4) link_BETA1-4 : angle 2.42238 ( 12) link_NAG-ASN : bond 0.00184 ( 4) link_NAG-ASN : angle 1.87704 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 0.582 Fit side-chains REVERT: A 176 ASP cc_start: 0.6731 (t0) cc_final: 0.6309 (t0) REVERT: A 283 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: A 322 ARG cc_start: 0.6991 (mtp-110) cc_final: 0.6558 (ttm110) REVERT: B 176 ASP cc_start: 0.6777 (t0) cc_final: 0.6346 (t0) REVERT: B 283 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: B 322 ARG cc_start: 0.6974 (mtp-110) cc_final: 0.6528 (ttm110) REVERT: B 324 PHE cc_start: 0.6265 (t80) cc_final: 0.6026 (t80) REVERT: C 176 ASP cc_start: 0.6725 (t0) cc_final: 0.6304 (t0) REVERT: C 283 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: C 322 ARG cc_start: 0.6934 (mtp-110) cc_final: 0.6507 (ttm110) REVERT: C 371 MET cc_start: 0.8320 (mtp) cc_final: 0.7863 (mtm) REVERT: D 176 ASP cc_start: 0.6696 (t0) cc_final: 0.6270 (t0) REVERT: D 283 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7771 (tt0) outliers start: 53 outliers final: 14 residues processed: 156 average time/residue: 0.5764 time to fit residues: 99.5848 Evaluate side-chains 134 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 68 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 169 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.147610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107261 restraints weight = 16103.439| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.71 r_work: 0.2874 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15480 Z= 0.112 Angle : 0.470 5.971 21004 Z= 0.256 Chirality : 0.039 0.125 2436 Planarity : 0.003 0.036 2568 Dihedral : 4.224 26.265 2208 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.45 % Allowed : 10.45 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.37 (0.19), residues: 1828 helix: 2.43 (0.15), residues: 1140 sheet: 1.50 (0.35), residues: 252 loop : -0.81 (0.25), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 146 TYR 0.014 0.001 TYR A 497 PHE 0.018 0.001 PHE C 324 TRP 0.008 0.001 TRP C 398 HIS 0.003 0.001 HIS D 234 Details of bonding type rmsd covalent geometry : bond 0.00226 (15472) covalent geometry : angle 0.46653 (20980) hydrogen bonds : bond 0.04642 ( 1036) hydrogen bonds : angle 4.34416 ( 3288) link_BETA1-4 : bond 0.00169 ( 4) link_BETA1-4 : angle 2.22086 ( 12) link_NAG-ASN : bond 0.00010 ( 4) link_NAG-ASN : angle 0.76897 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.598 Fit side-chains REVERT: A 175 VAL cc_start: 0.7324 (t) cc_final: 0.7089 (m) REVERT: A 176 ASP cc_start: 0.6963 (t0) cc_final: 0.6588 (t0) REVERT: A 322 ARG cc_start: 0.6899 (mtp-110) cc_final: 0.6431 (ttm110) REVERT: B 176 ASP cc_start: 0.6796 (t0) cc_final: 0.6489 (t0) REVERT: B 322 ARG cc_start: 0.6898 (mtp-110) cc_final: 0.6430 (ttm110) REVERT: C 176 ASP cc_start: 0.6738 (t0) cc_final: 0.6442 (t0) REVERT: C 322 ARG cc_start: 0.6856 (mtp-110) cc_final: 0.6391 (ttm110) REVERT: C 371 MET cc_start: 0.8279 (mtp) cc_final: 0.7956 (mtm) REVERT: D 176 ASP cc_start: 0.6718 (t0) cc_final: 0.6438 (t0) outliers start: 24 outliers final: 13 residues processed: 139 average time/residue: 0.5615 time to fit residues: 86.7074 Evaluate side-chains 134 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 99 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 181 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 174 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.147592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107210 restraints weight = 16260.075| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.71 r_work: 0.2866 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15480 Z= 0.114 Angle : 0.470 5.639 21004 Z= 0.256 Chirality : 0.039 0.126 2436 Planarity : 0.003 0.036 2568 Dihedral : 4.180 24.737 2208 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.51 % Allowed : 10.45 % Favored : 88.04 % 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: 2.43 (0.19), residues: 1828 helix: 2.48 (0.15), residues: 1140 sheet: 1.54 (0.34), residues: 252 loop : -0.80 (0.25), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.015 0.001 TYR D 497 PHE 0.029 0.001 PHE C 324 TRP 0.008 0.001 TRP B 398 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00234 (15472) covalent geometry : angle 0.46671 (20980) hydrogen bonds : bond 0.04659 ( 1036) hydrogen bonds : angle 4.32279 ( 3288) link_BETA1-4 : bond 0.00153 ( 4) link_BETA1-4 : angle 2.18789 ( 12) link_NAG-ASN : bond 0.00009 ( 4) link_NAG-ASN : angle 0.85379 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.567 Fit side-chains REVERT: A 176 ASP cc_start: 0.6944 (t0) cc_final: 0.6537 (t0) REVERT: A 322 ARG cc_start: 0.6907 (mtp-110) cc_final: 0.6435 (ttm110) REVERT: B 176 ASP cc_start: 0.6797 (t0) cc_final: 0.6482 (t0) REVERT: B 322 ARG cc_start: 0.6927 (mtp-110) cc_final: 0.6448 (ttm110) REVERT: C 176 ASP cc_start: 0.6735 (t0) cc_final: 0.6442 (t0) REVERT: C 322 ARG cc_start: 0.6862 (mtp-110) cc_final: 0.6392 (ttm110) REVERT: C 371 MET cc_start: 0.8289 (mtp) cc_final: 0.7975 (mtm) REVERT: D 176 ASP cc_start: 0.6713 (t0) cc_final: 0.6415 (t0) REVERT: D 324 PHE cc_start: 0.6075 (t80) cc_final: 0.5862 (t80) outliers start: 25 outliers final: 13 residues processed: 141 average time/residue: 0.5595 time to fit residues: 87.4053 Evaluate side-chains 133 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 53 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 180 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 327 GLN B 226 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.146581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105910 restraints weight = 16199.277| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.76 r_work: 0.2846 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15480 Z= 0.132 Angle : 0.495 6.188 21004 Z= 0.269 Chirality : 0.040 0.126 2436 Planarity : 0.003 0.035 2568 Dihedral : 4.272 24.330 2208 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.45 % Allowed : 10.57 % Favored : 87.98 % 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: 2.57 (0.19), residues: 1828 helix: 2.57 (0.15), residues: 1120 sheet: 1.57 (0.35), residues: 252 loop : -0.49 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 200 TYR 0.016 0.001 TYR D 497 PHE 0.030 0.001 PHE A 324 TRP 0.009 0.001 TRP D 398 HIS 0.003 0.001 HIS D 234 Details of bonding type rmsd covalent geometry : bond 0.00283 (15472) covalent geometry : angle 0.49138 (20980) hydrogen bonds : bond 0.05001 ( 1036) hydrogen bonds : angle 4.41622 ( 3288) link_BETA1-4 : bond 0.00101 ( 4) link_BETA1-4 : angle 2.24271 ( 12) link_NAG-ASN : bond 0.00069 ( 4) link_NAG-ASN : angle 1.19870 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.513 Fit side-chains REVERT: A 176 ASP cc_start: 0.6824 (t0) cc_final: 0.6446 (t0) REVERT: A 322 ARG cc_start: 0.6950 (mtp-110) cc_final: 0.6463 (ttm110) REVERT: B 176 ASP cc_start: 0.6810 (t0) cc_final: 0.6399 (t0) REVERT: B 322 ARG cc_start: 0.6943 (mtp-110) cc_final: 0.6463 (ttm110) REVERT: C 176 ASP cc_start: 0.6721 (t0) cc_final: 0.6424 (t0) REVERT: C 322 ARG cc_start: 0.6902 (mtp-110) cc_final: 0.6422 (ttm110) REVERT: C 371 MET cc_start: 0.8309 (mtp) cc_final: 0.7993 (mtm) REVERT: D 176 ASP cc_start: 0.6711 (t0) cc_final: 0.6315 (t0) REVERT: D 324 PHE cc_start: 0.6139 (t80) cc_final: 0.5937 (t80) outliers start: 24 outliers final: 14 residues processed: 154 average time/residue: 0.5569 time to fit residues: 95.0990 Evaluate side-chains 143 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.104689 restraints weight = 16219.034| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.73 r_work: 0.2828 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15480 Z= 0.164 Angle : 0.540 6.467 21004 Z= 0.292 Chirality : 0.042 0.132 2436 Planarity : 0.004 0.035 2568 Dihedral : 4.528 27.065 2208 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.57 % Allowed : 10.69 % Favored : 87.74 % 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: 2.45 (0.19), residues: 1828 helix: 2.50 (0.15), residues: 1116 sheet: 1.54 (0.35), residues: 252 loop : -0.61 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 200 TYR 0.016 0.002 TYR D 497 PHE 0.036 0.002 PHE C 324 TRP 0.011 0.002 TRP B 398 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00371 (15472) covalent geometry : angle 0.53607 (20980) hydrogen bonds : bond 0.05497 ( 1036) hydrogen bonds : angle 4.57209 ( 3288) link_BETA1-4 : bond 0.00027 ( 4) link_BETA1-4 : angle 2.37511 ( 12) link_NAG-ASN : bond 0.00149 ( 4) link_NAG-ASN : angle 1.65149 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.566 Fit side-chains REVERT: A 176 ASP cc_start: 0.6870 (t0) cc_final: 0.6458 (t0) REVERT: A 283 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: A 322 ARG cc_start: 0.6967 (mtp-110) cc_final: 0.6466 (ttm110) REVERT: B 176 ASP cc_start: 0.6761 (t0) cc_final: 0.6298 (t0) REVERT: B 283 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: B 322 ARG cc_start: 0.6952 (mtp-110) cc_final: 0.6466 (ttm110) REVERT: C 176 ASP cc_start: 0.6757 (t0) cc_final: 0.6328 (t0) REVERT: C 283 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: C 322 ARG cc_start: 0.6930 (mtp-110) cc_final: 0.6440 (ttm110) REVERT: C 371 MET cc_start: 0.8338 (mtp) cc_final: 0.7995 (mtm) REVERT: D 176 ASP cc_start: 0.6716 (t0) cc_final: 0.6271 (t0) REVERT: D 283 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: D 526 HIS cc_start: 0.6787 (m90) cc_final: 0.6564 (m170) outliers start: 26 outliers final: 14 residues processed: 150 average time/residue: 0.5384 time to fit residues: 89.8213 Evaluate side-chains 151 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 159 optimal weight: 6.9990 chunk 161 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 123 optimal weight: 0.0970 chunk 84 optimal weight: 7.9990 chunk 175 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS B 226 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.149295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109752 restraints weight = 16262.358| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.70 r_work: 0.2957 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15480 Z= 0.106 Angle : 0.461 6.181 21004 Z= 0.253 Chirality : 0.039 0.125 2436 Planarity : 0.003 0.036 2568 Dihedral : 4.028 21.913 2208 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.97 % Allowed : 11.11 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.49 (0.19), residues: 1828 helix: 2.54 (0.15), residues: 1140 sheet: 1.64 (0.35), residues: 252 loop : -0.85 (0.25), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.013 0.001 TYR A 497 PHE 0.039 0.001 PHE A 324 TRP 0.007 0.001 TRP B 398 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00207 (15472) covalent geometry : angle 0.45853 (20980) hydrogen bonds : bond 0.04315 ( 1036) hydrogen bonds : angle 4.21658 ( 3288) link_BETA1-4 : bond 0.00426 ( 4) link_BETA1-4 : angle 2.14190 ( 12) link_NAG-ASN : bond 0.00036 ( 4) link_NAG-ASN : angle 0.50814 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4609.26 seconds wall clock time: 79 minutes 40.09 seconds (4780.09 seconds total)