Starting phenix.real_space_refine on Fri Jul 3 16:38:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sq8_25379/07_2026/7sq8_25379_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sq8_25379/07_2026/7sq8_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_25379/07_2026/7sq8_25379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sq8_25379/07_2026/7sq8_25379.map" model { file = "/net/cci-nas-00/data/ceres_data/7sq8_25379/07_2026/7sq8_25379_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sq8_25379/07_2026/7sq8_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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15117 Number of models: 1 Model: "" Number of chains: 13 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: "B" 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: "C" 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: "D" 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: "F" 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: "G" 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: "H" 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, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 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} Time building chain proxies: 3.89, per 1000 atoms: 0.26 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: 1.34 Conformation dependent library (CDL) restraints added in 761.9 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: 0.72 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: 2.86 Time building geometry restraints manager: 1.83 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.010 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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/Z covalent geometry : bond 0.00351 / 0.19 (15472) covalent geometry : angle 0.55397 / 0.32 (20980) hydrogen bonds : bond 0.12909 / 8.32 ( 1036) hydrogen bonds : angle 6.50918 / 4.58 ( 3288) link_BETA1-4 : bond 0.00204 / 0.10 ( 4) link_BETA1-4 : angle 2.69937 / 1.30 ( 12) link_NAG-ASN : bond 0.00108 / 0.05 ( 4) link_NAG-ASN : angle 1.64545 / 0.92 ( 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 : 0.804 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: 0.6338 (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: 0.5296 time to fit residues: 111.8635 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 : 0.390 ------------------------------------------------------------------------------- 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... 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 = 0.3640 r_free = 0.3640 target = 0.143949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.103448 restraints weight = 16200.013| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.61 r_work: 0.2825 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.0988 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 : 0.583 4.791 21004 Z= 0.316 Chirality : 0.044 0.142 2436 Planarity : 0.004 0.033 2568 Dihedral : 4.903 34.475 2208 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.36 % Allowed : 5.74 % Favored : 91.91 % 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: 2.02 (0.19), residues: 1828 helix: 2.09 (0.15), residues: 1120 sheet: 1.05 (0.34), residues: 252 loop : -0.37 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 200 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 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (15472) covalent geometry : angle 0.57892 / 0.32 (20980) hydrogen bonds : bond 0.06181 / 4.16 ( 1036) hydrogen bonds : angle 5.06005 / 3.58 ( 3288) link_BETA1-4 : bond 0.00171 / 0.08 ( 4) link_BETA1-4 : angle 2.31074 / 1.12 ( 12) link_NAG-ASN : bond 0.00379 / 0.19 ( 4) link_NAG-ASN : angle 1.95206 / 1.06 ( 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 171 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.514 Fit side-chains REVERT: A 322 ARG cc_start: 0.6893 (mtp-110) cc_final: 0.6433 (ttm170) REVERT: A 324 PHE cc_start: 0.6219 (t80) cc_final: 0.5905 (t80) REVERT: A 483 GLN cc_start: 0.6089 (OUTLIER) cc_final: 0.4513 (mm110) REVERT: B 322 ARG cc_start: 0.6881 (mtp-110) cc_final: 0.6413 (ttm170) REVERT: B 324 PHE cc_start: 0.6187 (t80) cc_final: 0.5877 (t80) REVERT: B 483 GLN cc_start: 0.6089 (OUTLIER) cc_final: 0.4521 (mm110) REVERT: C 322 ARG cc_start: 0.6831 (mtp-110) cc_final: 0.6420 (ttm110) REVERT: C 324 PHE cc_start: 0.6166 (t80) cc_final: 0.5855 (t80) REVERT: C 483 GLN cc_start: 0.6096 (OUTLIER) cc_final: 0.4539 (mm-40) REVERT: D 324 PHE cc_start: 0.6226 (t80) cc_final: 0.5875 (t80) REVERT: D 483 GLN cc_start: 0.6090 (OUTLIER) cc_final: 0.4521 (mm-40) outliers start: 39 outliers final: 16 residues processed: 158 average time/residue: 0.4988 time to fit residues: 88.1903 Evaluate side-chains 143 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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: 8.9990 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 469 ASN B 469 ASN C 469 ASN D 469 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.105235 restraints weight = 16208.107| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.75 r_work: 0.2844 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15480 Z= 0.133 Angle : 0.501 4.729 21004 Z= 0.274 Chirality : 0.040 0.129 2436 Planarity : 0.003 0.032 2568 Dihedral : 4.524 30.988 2208 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.29 % Allowed : 6.70 % Favored : 91.00 % 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: 2.33 (0.15), residues: 1120 sheet: 1.24 (0.35), residues: 252 loop : -0.35 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 200 TYR 0.015 0.001 TYR D 497 PHE 0.015 0.001 PHE A 350 TRP 0.010 0.001 TRP C 398 HIS 0.003 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (15472) covalent geometry : angle 0.49747 / 0.27 (20980) hydrogen bonds : bond 0.05238 / 3.53 ( 1036) hydrogen bonds : angle 4.68224 / 3.33 ( 3288) link_BETA1-4 : bond 0.00172 / 0.08 ( 4) link_BETA1-4 : angle 2.13092 / 1.07 ( 12) link_NAG-ASN : bond 0.00106 / 0.05 ( 4) link_NAG-ASN : angle 1.24184 / 0.68 ( 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 162 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.604 Fit side-chains REVERT: A 322 ARG cc_start: 0.6872 (mtp-110) cc_final: 0.6464 (ttm110) REVERT: A 324 PHE cc_start: 0.6185 (t80) cc_final: 0.5901 (t80) REVERT: A 483 GLN cc_start: 0.5193 (OUTLIER) cc_final: 0.3855 (mm110) REVERT: B 322 ARG cc_start: 0.6859 (mtp-110) cc_final: 0.6446 (ttm110) REVERT: B 324 PHE cc_start: 0.6155 (t80) cc_final: 0.5870 (t80) REVERT: B 483 GLN cc_start: 0.5228 (OUTLIER) cc_final: 0.3892 (mm110) REVERT: C 322 ARG cc_start: 0.6828 (mtp-110) cc_final: 0.6423 (ttm110) REVERT: C 324 PHE cc_start: 0.6142 (t80) cc_final: 0.5860 (t80) REVERT: C 483 GLN cc_start: 0.5173 (OUTLIER) cc_final: 0.3883 (mm110) REVERT: D 324 PHE cc_start: 0.6194 (t80) cc_final: 0.5866 (t80) REVERT: D 371 MET cc_start: 0.8213 (mtp) cc_final: 0.7808 (mtm) REVERT: D 483 GLN cc_start: 0.5188 (OUTLIER) cc_final: 0.3872 (mm110) REVERT: D 526 HIS cc_start: 0.6789 (m90) cc_final: 0.6577 (m170) outliers start: 38 outliers final: 16 residues processed: 154 average time/residue: 0.4822 time to fit residues: 83.5873 Evaluate side-chains 140 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 10 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.145011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103679 restraints weight = 16210.191| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.75 r_work: 0.2822 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15480 Z= 0.164 Angle : 0.536 5.813 21004 Z= 0.290 Chirality : 0.042 0.135 2436 Planarity : 0.004 0.032 2568 Dihedral : 4.672 31.340 2208 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.05 % Allowed : 8.27 % Favored : 89.67 % 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: 2.27 (0.19), residues: 1828 helix: 2.33 (0.15), residues: 1116 sheet: 1.29 (0.34), residues: 252 loop : -0.48 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 200 TYR 0.016 0.001 TYR D 497 PHE 0.014 0.002 PHE D 350 TRP 0.012 0.002 TRP A 398 HIS 0.004 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (15472) covalent geometry : angle 0.53180 / 0.29 (20980) hydrogen bonds : bond 0.05627 / 3.79 ( 1036) hydrogen bonds : angle 4.72688 / 3.35 ( 3288) link_BETA1-4 : bond 0.00019 / 0.01 ( 4) link_BETA1-4 : angle 2.30959 / 1.13 ( 12) link_NAG-ASN : bond 0.00183 / 0.09 ( 4) link_NAG-ASN : angle 1.67352 / 0.91 ( 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 164 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.593 Fit side-chains REVERT: A 322 ARG cc_start: 0.6943 (mtp-110) cc_final: 0.6516 (ttm110) REVERT: A 324 PHE cc_start: 0.6204 (t80) cc_final: 0.5947 (t80) REVERT: B 322 ARG cc_start: 0.6926 (mtp-110) cc_final: 0.6483 (ttm110) REVERT: B 324 PHE cc_start: 0.6197 (t80) cc_final: 0.5929 (t80) REVERT: B 371 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8030 (mtm) REVERT: C 322 ARG cc_start: 0.6890 (mtp-110) cc_final: 0.6456 (ttm110) REVERT: C 324 PHE cc_start: 0.6174 (t80) cc_final: 0.5904 (t80) REVERT: C 371 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8025 (mtm) REVERT: D 324 PHE cc_start: 0.6216 (t80) cc_final: 0.5938 (t80) outliers start: 34 outliers final: 17 residues processed: 153 average time/residue: 0.4836 time to fit residues: 82.8815 Evaluate side-chains 139 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 371 MET 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: 0.9990 chunk 110 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.145151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104274 restraints weight = 16293.860| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.73 r_work: 0.2832 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15480 Z= 0.147 Angle : 0.518 6.039 21004 Z= 0.281 Chirality : 0.041 0.131 2436 Planarity : 0.004 0.034 2568 Dihedral : 4.570 30.801 2208 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.87 % Allowed : 9.54 % Favored : 88.59 % 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: 1.34 (0.34), residues: 252 loop : -0.43 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 200 TYR 0.015 0.001 TYR D 497 PHE 0.013 0.001 PHE C 474 TRP 0.011 0.001 TRP B 398 HIS 0.003 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (15472) covalent geometry : angle 0.51453 / 0.28 (20980) hydrogen bonds : bond 0.05363 / 3.62 ( 1036) hydrogen bonds : angle 4.60527 / 3.26 ( 3288) link_BETA1-4 : bond 0.00079 / 0.04 ( 4) link_BETA1-4 : angle 2.32602 / 1.15 ( 12) link_NAG-ASN : bond 0.00142 / 0.07 ( 4) link_NAG-ASN : angle 1.47921 / 0.80 ( 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 167 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.551 Fit side-chains REVERT: A 176 ASP cc_start: 0.6697 (t0) cc_final: 0.6301 (t0) REVERT: A 322 ARG cc_start: 0.6940 (mtp-110) cc_final: 0.6508 (ttm110) REVERT: A 324 PHE cc_start: 0.6223 (t80) cc_final: 0.5990 (t80) REVERT: B 176 ASP cc_start: 0.6717 (t0) cc_final: 0.6338 (t0) REVERT: B 322 ARG cc_start: 0.6917 (mtp-110) cc_final: 0.6477 (ttm110) REVERT: B 324 PHE cc_start: 0.6248 (t80) cc_final: 0.5988 (t80) REVERT: B 371 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8031 (mtm) REVERT: C 176 ASP cc_start: 0.6694 (t0) cc_final: 0.6298 (t0) REVERT: C 322 ARG cc_start: 0.6874 (mtp-110) cc_final: 0.6455 (ttm110) REVERT: C 324 PHE cc_start: 0.6236 (t80) cc_final: 0.5973 (t80) REVERT: C 371 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8047 (mtm) REVERT: D 176 ASP cc_start: 0.6678 (t0) cc_final: 0.6282 (t0) REVERT: D 526 HIS cc_start: 0.6742 (m90) cc_final: 0.6534 (m170) outliers start: 31 outliers final: 17 residues processed: 154 average time/residue: 0.4858 time to fit residues: 84.1561 Evaluate side-chains 138 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 371 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 146 optimal weight: 0.0870 chunk 180 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS B 226 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.104193 restraints weight = 16166.438| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.72 r_work: 0.2822 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15480 Z= 0.165 Angle : 0.543 6.175 21004 Z= 0.293 Chirality : 0.042 0.133 2436 Planarity : 0.004 0.033 2568 Dihedral : 4.678 30.140 2208 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.66 % Allowed : 9.30 % 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: 2.28 (0.19), residues: 1828 helix: 2.35 (0.15), residues: 1116 sheet: 1.33 (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 A 200 TYR 0.016 0.002 TYR C 497 PHE 0.014 0.002 PHE C 235 TRP 0.012 0.002 TRP C 398 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (15472) covalent geometry : angle 0.53891 / 0.29 (20980) hydrogen bonds : bond 0.05624 / 3.79 ( 1036) hydrogen bonds : angle 4.66276 / 3.31 ( 3288) link_BETA1-4 : bond 0.00055 / 0.03 ( 4) link_BETA1-4 : angle 2.41013 / 1.18 ( 12) link_NAG-ASN : bond 0.00192 / 0.10 ( 4) link_NAG-ASN : angle 1.76839 / 0.96 ( 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 171 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.600 Fit side-chains REVERT: A 176 ASP cc_start: 0.6709 (t0) cc_final: 0.6262 (t0) REVERT: A 283 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: A 322 ARG cc_start: 0.6953 (mtp-110) cc_final: 0.6523 (ttm110) REVERT: A 324 PHE cc_start: 0.6215 (t80) cc_final: 0.5995 (t80) REVERT: B 176 ASP cc_start: 0.6733 (t0) cc_final: 0.6284 (t0) REVERT: B 283 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: B 322 ARG cc_start: 0.6948 (mtp-110) cc_final: 0.6508 (ttm110) REVERT: B 324 PHE cc_start: 0.6249 (t80) cc_final: 0.6024 (t80) REVERT: B 371 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8073 (mtm) REVERT: C 141 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8513 (pm20) REVERT: C 176 ASP cc_start: 0.6707 (t0) cc_final: 0.6253 (t0) REVERT: C 283 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: C 322 ARG cc_start: 0.6911 (mtp-110) cc_final: 0.6432 (ttm110) REVERT: C 371 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8058 (mtm) REVERT: D 176 ASP cc_start: 0.6693 (t0) cc_final: 0.6240 (t0) REVERT: D 283 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7774 (tt0) outliers start: 44 outliers final: 17 residues processed: 151 average time/residue: 0.5699 time to fit residues: 95.8341 Evaluate side-chains 144 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 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 283 GLU 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 141 GLU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 371 MET 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 283 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS 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 = 0.3667 r_free = 0.3667 target = 0.146143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.105567 restraints weight = 16107.325| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.71 r_work: 0.2857 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15480 Z= 0.133 Angle : 0.504 6.192 21004 Z= 0.273 Chirality : 0.040 0.128 2436 Planarity : 0.003 0.035 2568 Dihedral : 4.456 28.959 2208 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.93 % Allowed : 9.90 % 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: 2.44 (0.19), residues: 1828 helix: 2.46 (0.15), residues: 1120 sheet: 1.41 (0.35), residues: 252 loop : -0.45 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.015 0.001 TYR A 497 PHE 0.013 0.001 PHE C 474 TRP 0.010 0.001 TRP B 398 HIS 0.003 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15472) covalent geometry : angle 0.49978 / 0.27 (20980) hydrogen bonds : bond 0.05124 / 3.46 ( 1036) hydrogen bonds : angle 4.51155 / 3.20 ( 3288) link_BETA1-4 : bond 0.00085 / 0.04 ( 4) link_BETA1-4 : angle 2.31541 / 1.15 ( 12) link_NAG-ASN : bond 0.00106 / 0.05 ( 4) link_NAG-ASN : angle 1.29376 / 0.70 ( 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 155 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.581 Fit side-chains REVERT: A 176 ASP cc_start: 0.6800 (t0) cc_final: 0.6387 (t0) REVERT: A 283 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: A 322 ARG cc_start: 0.6969 (mtp-110) cc_final: 0.6505 (ttm110) REVERT: B 176 ASP cc_start: 0.6789 (t0) cc_final: 0.6376 (t0) REVERT: B 283 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: B 322 ARG cc_start: 0.6971 (mtp-110) cc_final: 0.6495 (ttm110) REVERT: B 371 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8071 (mtm) REVERT: C 176 ASP cc_start: 0.6789 (t0) cc_final: 0.6382 (t0) REVERT: C 283 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: C 322 ARG cc_start: 0.6924 (mtp-110) cc_final: 0.6464 (ttm110) REVERT: C 371 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8048 (mtm) REVERT: D 176 ASP cc_start: 0.6771 (t0) cc_final: 0.6361 (t0) REVERT: D 283 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7716 (tt0) outliers start: 32 outliers final: 16 residues processed: 138 average time/residue: 0.5566 time to fit residues: 85.5028 Evaluate side-chains 137 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 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 283 GLU 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 283 GLU Chi-restraints excluded: chain C residue 371 MET 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 283 GLU Chi-restraints excluded: chain D residue 472 ASP 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: 7.9990 chunk 10 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 174 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN 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 = 0.3658 r_free = 0.3658 target = 0.145374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.104610 restraints weight = 16241.383| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.71 r_work: 0.2819 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15480 Z= 0.155 Angle : 0.529 6.053 21004 Z= 0.286 Chirality : 0.041 0.130 2436 Planarity : 0.004 0.035 2568 Dihedral : 4.592 29.881 2208 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.75 % Allowed : 10.14 % 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: 2.41 (0.15), residues: 1120 sheet: 1.39 (0.34), residues: 252 loop : -0.51 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 200 TYR 0.016 0.001 TYR B 497 PHE 0.020 0.002 PHE C 324 TRP 0.011 0.002 TRP B 398 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (15472) covalent geometry : angle 0.52487 / 0.29 (20980) hydrogen bonds : bond 0.05439 / 3.67 ( 1036) hydrogen bonds : angle 4.58978 / 3.26 ( 3288) link_BETA1-4 : bond 0.00058 / 0.03 ( 4) link_BETA1-4 : angle 2.37684 / 1.17 ( 12) link_NAG-ASN : bond 0.00154 / 0.08 ( 4) link_NAG-ASN : angle 1.63104 / 0.88 ( 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 159 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.447 Fit side-chains REVERT: A 176 ASP cc_start: 0.6800 (t0) cc_final: 0.6317 (t0) REVERT: A 283 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: A 322 ARG cc_start: 0.6955 (mtp-110) cc_final: 0.6479 (ttm110) REVERT: B 176 ASP cc_start: 0.6762 (t0) cc_final: 0.6315 (t0) REVERT: B 283 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: B 322 ARG cc_start: 0.6949 (mtp-110) cc_final: 0.6469 (ttm110) REVERT: B 371 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8096 (mtm) REVERT: C 176 ASP cc_start: 0.6731 (t0) cc_final: 0.6286 (t0) REVERT: C 283 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: C 322 ARG cc_start: 0.6919 (mtp-110) cc_final: 0.6452 (ttm110) REVERT: C 371 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8087 (mtm) REVERT: D 176 ASP cc_start: 0.6737 (t0) cc_final: 0.6292 (t0) REVERT: D 283 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: D 324 PHE cc_start: 0.6129 (t80) cc_final: 0.5926 (t80) REVERT: D 526 HIS cc_start: 0.6759 (m90) cc_final: 0.6553 (m170) outliers start: 29 outliers final: 16 residues processed: 147 average time/residue: 0.5097 time to fit residues: 83.7734 Evaluate side-chains 148 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 283 GLU 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 283 GLU Chi-restraints excluded: chain C residue 371 MET 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 283 GLU Chi-restraints excluded: chain D residue 472 ASP 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: 8.9990 chunk 44 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.143422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.102545 restraints weight = 16250.730| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.71 r_work: 0.2813 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15480 Z= 0.237 Angle : 0.626 6.669 21004 Z= 0.335 Chirality : 0.046 0.142 2436 Planarity : 0.005 0.035 2568 Dihedral : 5.038 29.043 2208 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.81 % Allowed : 10.57 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.19), residues: 1828 helix: 2.22 (0.15), residues: 1116 sheet: 1.29 (0.33), residues: 252 loop : -0.76 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 200 TYR 0.016 0.002 TYR A 497 PHE 0.018 0.002 PHE C 493 TRP 0.014 0.002 TRP B 398 HIS 0.004 0.002 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.24 (15472) covalent geometry : angle 0.62074 / 0.33 (20980) hydrogen bonds : bond 0.06382 / 4.30 ( 1036) hydrogen bonds : angle 4.84485 / 3.44 ( 3288) link_BETA1-4 : bond 0.00054 / 0.03 ( 4) link_BETA1-4 : angle 2.68691 / 1.28 ( 12) link_NAG-ASN : bond 0.00287 / 0.14 ( 4) link_NAG-ASN : angle 2.39940 / 1.30 ( 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 154 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.627 Fit side-chains REVERT: A 176 ASP cc_start: 0.6851 (t0) cc_final: 0.6375 (t0) REVERT: A 283 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: A 322 ARG cc_start: 0.7065 (mtp-110) cc_final: 0.6582 (ttm110) REVERT: B 176 ASP cc_start: 0.6859 (t0) cc_final: 0.6387 (t0) REVERT: B 283 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: B 322 ARG cc_start: 0.7048 (mtp-110) cc_final: 0.6560 (ttm110) REVERT: B 371 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8105 (mtm) REVERT: C 141 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8555 (pm20) REVERT: C 176 ASP cc_start: 0.6840 (t0) cc_final: 0.6373 (t0) REVERT: C 283 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: C 322 ARG cc_start: 0.7021 (mtp-110) cc_final: 0.6554 (ttm110) REVERT: C 371 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8079 (mtm) REVERT: D 176 ASP cc_start: 0.6839 (t0) cc_final: 0.6371 (t0) REVERT: D 283 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7836 (tt0) outliers start: 30 outliers final: 17 residues processed: 143 average time/residue: 0.5067 time to fit residues: 80.9511 Evaluate side-chains 147 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 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 283 GLU 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 283 GLU 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 141 GLU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 371 MET 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 283 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.104428 restraints weight = 16223.798| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.72 r_work: 0.2839 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15480 Z= 0.153 Angle : 0.538 6.767 21004 Z= 0.291 Chirality : 0.041 0.130 2436 Planarity : 0.004 0.035 2568 Dihedral : 4.628 28.378 2208 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 2.26 (0.19), residues: 1828 helix: 2.37 (0.15), residues: 1120 sheet: 1.37 (0.34), residues: 252 loop : -0.69 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 200 TYR 0.016 0.001 TYR A 497 PHE 0.031 0.002 PHE A 324 TRP 0.011 0.001 TRP B 398 HIS 0.004 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (15472) covalent geometry : angle 0.53334 / 0.29 (20980) hydrogen bonds : bond 0.05443 / 3.68 ( 1036) hydrogen bonds : angle 4.62038 / 3.28 ( 3288) link_BETA1-4 : bond 0.00063 / 0.03 ( 4) link_BETA1-4 : angle 2.44781 / 1.20 ( 12) link_NAG-ASN : bond 0.00160 / 0.08 ( 4) link_NAG-ASN : angle 1.59372 / 0.87 ( 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 158 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.593 Fit side-chains REVERT: A 176 ASP cc_start: 0.6823 (t0) cc_final: 0.6373 (t0) REVERT: A 283 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: A 322 ARG cc_start: 0.6963 (mtp-110) cc_final: 0.6497 (ttm110) REVERT: B 176 ASP cc_start: 0.6809 (t0) cc_final: 0.6374 (t0) REVERT: B 283 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: B 322 ARG cc_start: 0.6933 (mtp-110) cc_final: 0.6461 (ttm110) REVERT: B 371 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8127 (mtm) REVERT: C 141 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: C 176 ASP cc_start: 0.6790 (t0) cc_final: 0.6357 (t0) REVERT: C 283 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: C 322 ARG cc_start: 0.6920 (mtp-110) cc_final: 0.6448 (ttm110) REVERT: C 371 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8088 (mtm) REVERT: D 176 ASP cc_start: 0.6768 (t0) cc_final: 0.6325 (t0) REVERT: D 283 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: D 526 HIS cc_start: 0.6807 (m90) cc_final: 0.6601 (m170) outliers start: 26 outliers final: 16 residues processed: 147 average time/residue: 0.5359 time to fit residues: 87.9732 Evaluate side-chains 149 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 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 283 GLU 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 283 GLU 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 141 GLU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 371 MET 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 283 GLU Chi-restraints excluded: chain D residue 472 ASP 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: 10.0000 chunk 78 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 123 optimal weight: 0.2980 chunk 84 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.148076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.107640 restraints weight = 16334.683| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.80 r_work: 0.2896 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15480 Z= 0.115 Angle : 0.485 6.873 21004 Z= 0.264 Chirality : 0.039 0.128 2436 Planarity : 0.003 0.036 2568 Dihedral : 4.209 25.251 2208 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.27 % Allowed : 11.11 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.19), residues: 1828 helix: 2.45 (0.15), residues: 1140 sheet: 1.55 (0.35), residues: 252 loop : -0.98 (0.24), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 200 TYR 0.014 0.001 TYR A 497 PHE 0.038 0.001 PHE C 324 TRP 0.008 0.001 TRP B 398 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (15472) covalent geometry : angle 0.48198 / 0.26 (20980) hydrogen bonds : bond 0.04621 / 3.12 ( 1036) hydrogen bonds : angle 4.32569 / 3.07 ( 3288) link_BETA1-4 : bond 0.00179 / 0.09 ( 4) link_BETA1-4 : angle 2.24941 / 1.13 ( 12) link_NAG-ASN : bond 0.00003 / 0.00 ( 4) link_NAG-ASN : angle 0.80882 / 0.45 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4394.89 seconds wall clock time: 75 minutes 55.32 seconds (4555.32 seconds total)