Starting phenix.real_space_refine on Sat Sep 12 11:06:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sq7_25378/09_2026/7sq7_25378_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sq7_25378/09_2026/7sq7_25378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sq7_25378/09_2026/7sq7_25378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sq7_25378/09_2026/7sq7_25378.map" model { file = "/net/cci-nas-00/data/ceres_data/7sq7_25378/09_2026/7sq7_25378_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sq7_25378/09_2026/7sq7_25378_neut_trim.cif" } resolution = 2.41 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= 0.008 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 96 5.16 5 Na 1 4.78 5 C 10004 2.51 5 N 2500 2.21 5 O 2692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15305 Number of models: 1 Model: "" Number of chains: 16 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: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {' NA': 1, 'EUJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'EUJ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'EUJ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'EUJ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.45, per 1000 atoms: 0.23 Number of scatterers: 15305 At special positions: 0 Unit cell: (115.37, 115.37, 112.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 12 15.00 Na 1 11.00 O 2692 8.00 N 2500 7.00 C 10004 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: 1.20 Conformation dependent library (CDL) restraints added in 560.9 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: 80 helices and 12 sheets defined 68.0% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 51 through 58 removed outlier: 3.771A pdb=" N ARG A 57 " --> pdb=" O CYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 106 Processing helix chain 'A' and resid 121 through 138 removed outlier: 3.502A pdb=" N ILE A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 241 through 248 removed outlier: 3.778A pdb=" N LEU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 338 removed outlier: 3.769A pdb=" N VAL A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 removed outlier: 3.692A pdb=" N GLU A 349 " --> pdb=" O TRP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 377 Processing helix chain 'A' and resid 382 through 400 Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.633A pdb=" N LEU A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 448 removed outlier: 4.047A pdb=" N LEU A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 3.759A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 4.161A 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 483 removed outlier: 3.672A pdb=" N THR A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' 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: 3.771A pdb=" N ARG B 57 " --> pdb=" O CYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 106 Processing helix chain 'B' and resid 121 through 138 removed outlier: 3.502A pdb=" N ILE B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 241 through 248 removed outlier: 3.778A pdb=" N LEU B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 338 removed outlier: 3.769A pdb=" N VAL B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 349 removed outlier: 3.692A pdb=" N GLU B 349 " --> pdb=" O TRP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 377 Processing helix chain 'B' and resid 382 through 400 Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.632A pdb=" N LEU B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 448 removed outlier: 4.047A pdb=" N LEU B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 3.759A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 4.161A 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 483 removed outlier: 3.673A pdb=" N THR B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 486 No H-bonds generated for 'chain 'B' and resid 484 through 486' 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: 3.771A pdb=" N ARG C 57 " --> pdb=" O CYS C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 106 Processing helix chain 'C' and resid 121 through 138 removed outlier: 3.502A pdb=" N ILE C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 241 through 248 removed outlier: 3.778A pdb=" N LEU C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 338 removed outlier: 3.769A pdb=" N VAL C 332 " --> pdb=" O ASN C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 349 removed outlier: 3.691A pdb=" N GLU C 349 " --> pdb=" O TRP C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 377 Processing helix chain 'C' and resid 382 through 400 Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.632A pdb=" N LEU C 405 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 448 removed outlier: 4.047A pdb=" N LEU C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 3.759A pdb=" N VAL C 434 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 removed outlier: 4.161A 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 483 removed outlier: 3.673A pdb=" N THR C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 486 No H-bonds generated for 'chain 'C' and resid 484 through 486' 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: 3.771A pdb=" N ARG D 57 " --> pdb=" O CYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 106 Processing helix chain 'D' and resid 121 through 138 removed outlier: 3.502A pdb=" N ILE D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 241 through 248 removed outlier: 3.778A pdb=" N LEU D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 338 removed outlier: 3.769A pdb=" N VAL D 332 " --> pdb=" O ASN D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 349 removed outlier: 3.691A pdb=" N GLU D 349 " --> pdb=" O TRP D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 377 Processing helix chain 'D' and resid 382 through 400 Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.632A pdb=" N LEU D 405 " --> pdb=" O VAL D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 448 removed outlier: 4.047A pdb=" N LEU D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 3.759A pdb=" N VAL D 434 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 removed outlier: 4.161A 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 483 removed outlier: 3.673A pdb=" N THR D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 486 No H-bonds generated for 'chain 'D' and resid 484 through 486' 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 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 6.815A pdb=" N ARG A 168 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 231 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS A 166 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE A 233 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA A 164 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.593A 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 Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.816A pdb=" N ARG B 168 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL B 231 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS B 166 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE B 233 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 164 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.593A 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 Processing sheet with id=AA7, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'C' and resid 118 through 119 removed outlier: 6.815A pdb=" N ARG C 168 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL C 231 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS C 166 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE C 233 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 164 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.594A 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 Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'D' and resid 118 through 119 removed outlier: 6.814A pdb=" N ARG D 168 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL D 231 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS D 166 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE D 233 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA D 164 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.593A 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 1132 hydrogen bonds defined for protein. 3276 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: 2.39 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2707 1.32 - 1.45: 4133 1.45 - 1.57: 8652 1.57 - 1.69: 36 1.69 - 1.82: 132 Bond restraints: 15660 Sorted by residual: bond pdb=" O3 EUJ D 601 " pdb=" P3 EUJ D 601 " ideal model delta sigma weight residual 1.727 1.611 0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" O3 EUJ C 601 " pdb=" P3 EUJ C 601 " ideal model delta sigma weight residual 1.727 1.611 0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" O3 EUJ B 601 " pdb=" P3 EUJ B 601 " ideal model delta sigma weight residual 1.727 1.612 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" O3 EUJ A 601 " pdb=" P3 EUJ A 601 " ideal model delta sigma weight residual 1.727 1.612 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" O12 EUJ C 601 " pdb=" P1 EUJ C 601 " ideal model delta sigma weight residual 1.497 1.606 -0.109 2.00e-02 2.50e+03 2.96e+01 ... (remaining 15655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 20475 2.48 - 4.97: 661 4.97 - 7.45: 72 7.45 - 9.93: 16 9.93 - 12.41: 16 Bond angle restraints: 21240 Sorted by residual: angle pdb=" O11 EUJ C 601 " pdb=" P1 EUJ C 601 " pdb=" O12 EUJ C 601 " ideal model delta sigma weight residual 121.88 109.47 12.41 3.00e+00 1.11e-01 1.71e+01 angle pdb=" O11 EUJ D 601 " pdb=" P1 EUJ D 601 " pdb=" O12 EUJ D 601 " ideal model delta sigma weight residual 121.88 109.47 12.41 3.00e+00 1.11e-01 1.71e+01 angle pdb=" O11 EUJ A 601 " pdb=" P1 EUJ A 601 " pdb=" O12 EUJ A 601 " ideal model delta sigma weight residual 121.88 109.47 12.41 3.00e+00 1.11e-01 1.71e+01 angle pdb=" O11 EUJ B 601 " pdb=" P1 EUJ B 601 " pdb=" O12 EUJ B 601 " ideal model delta sigma weight residual 121.88 109.47 12.41 3.00e+00 1.11e-01 1.71e+01 angle pdb=" C5 EUJ A 601 " pdb=" O5 EUJ A 601 " pdb=" P5 EUJ A 601 " ideal model delta sigma weight residual 113.41 124.93 -11.52 3.00e+00 1.11e-01 1.48e+01 ... (remaining 21235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.92: 9056 33.92 - 67.85: 320 67.85 - 101.77: 48 101.77 - 135.70: 4 135.70 - 169.62: 4 Dihedral angle restraints: 9432 sinusoidal: 3996 harmonic: 5436 Sorted by residual: dihedral pdb=" C1 EUJ B 601 " pdb=" O1 EUJ B 601 " pdb=" P1 EUJ B 601 " pdb=" O12 EUJ B 601 " ideal model delta sinusoidal sigma weight residual 184.61 14.99 169.62 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 EUJ C 601 " pdb=" O1 EUJ C 601 " pdb=" P1 EUJ C 601 " pdb=" O12 EUJ C 601 " ideal model delta sinusoidal sigma weight residual 184.61 14.99 169.62 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 EUJ D 601 " pdb=" O1 EUJ D 601 " pdb=" P1 EUJ D 601 " pdb=" O12 EUJ D 601 " ideal model delta sinusoidal sigma weight residual 184.61 14.99 169.62 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 9429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2156 0.091 - 0.183: 244 0.183 - 0.274: 52 0.274 - 0.366: 8 0.366 - 0.457: 4 Chirality restraints: 2464 Sorted by residual: chirality pdb=" C2C EUJ A 601 " pdb=" C1C EUJ A 601 " pdb=" C3C EUJ A 601 " pdb=" O2C EUJ A 601 " both_signs ideal model delta sigma weight residual False -2.16 -2.62 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" C2C EUJ B 601 " pdb=" C1C EUJ B 601 " pdb=" C3C EUJ B 601 " pdb=" O2C EUJ B 601 " both_signs ideal model delta sigma weight residual False -2.16 -2.62 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" C2C EUJ C 601 " pdb=" C1C EUJ C 601 " pdb=" C3C EUJ C 601 " pdb=" O2C EUJ C 601 " both_signs ideal model delta sigma weight residual False -2.16 -2.62 0.46 2.00e-01 2.50e+01 5.23e+00 ... (remaining 2461 not shown) Planarity restraints: 2580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 481 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C GLN D 481 " -0.056 2.00e-02 2.50e+03 pdb=" O GLN D 481 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA D 482 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 481 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C GLN C 481 " 0.056 2.00e-02 2.50e+03 pdb=" O GLN C 481 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 482 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 481 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C GLN B 481 " 0.056 2.00e-02 2.50e+03 pdb=" O GLN B 481 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA B 482 " -0.019 2.00e-02 2.50e+03 ... (remaining 2577 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2907 2.78 - 3.31: 14933 3.31 - 3.84: 26120 3.84 - 4.37: 32106 4.37 - 4.90: 52331 Nonbonded interactions: 128397 Sorted by model distance: nonbonded pdb=" OH TYR C 450 " pdb=" OD1 ASP D 384 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR B 450 " pdb=" OD1 ASP C 384 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR A 450 " pdb=" OD1 ASP B 384 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASP A 384 " pdb=" OH TYR D 450 " model vdw 2.263 3.040 nonbonded pdb=" NZ LYS C 65 " pdb=" OG SER C 319 " model vdw 2.342 3.120 ... (remaining 128392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 601) selection = chain 'B' selection = chain 'C' 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.650 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.009 0.116 15668 Z= 0.522 Angle : 1.022 12.413 21264 Z= 0.623 Chirality : 0.066 0.457 2464 Planarity : 0.005 0.049 2576 Dihedral : 17.540 169.620 5928 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % 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: 0.91 (0.20), residues: 1828 helix: 1.24 (0.15), residues: 1088 sheet: 0.37 (0.35), residues: 252 loop : -0.57 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 270 TYR 0.012 0.002 TYR B 131 PHE 0.018 0.002 PHE A 477 TRP 0.021 0.002 TRP B 491 HIS 0.004 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00861 / 0.52 (15660) covalent geometry : angle 1.01462 / 0.62 (21240) hydrogen bonds : bond 0.20441 / 13.58 ( 1040) hydrogen bonds : angle 7.45402 / 5.34 ( 3276) link_BETA1-4 : bond 0.00566 / 0.28 ( 4) link_BETA1-4 : angle 3.65894 / 1.82 ( 12) link_NAG-ASN : bond 0.00071 / 0.04 ( 4) link_NAG-ASN : angle 3.89913 / 2.26 ( 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 240 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.580 Fit side-chains REVERT: A 54 ASP cc_start: 0.6501 (m-30) cc_final: 0.6091 (m-30) REVERT: A 74 LEU cc_start: 0.8171 (tp) cc_final: 0.7918 (tt) REVERT: A 280 HIS cc_start: 0.7801 (t70) cc_final: 0.7303 (t70) REVERT: A 300 LEU cc_start: 0.7569 (tp) cc_final: 0.7140 (mt) REVERT: A 321 LEU cc_start: 0.7293 (tp) cc_final: 0.6882 (tp) REVERT: B 74 LEU cc_start: 0.8165 (tp) cc_final: 0.7908 (tt) REVERT: B 280 HIS cc_start: 0.7802 (t70) cc_final: 0.7281 (t70) REVERT: B 300 LEU cc_start: 0.7592 (tp) cc_final: 0.7146 (mt) REVERT: B 321 LEU cc_start: 0.7286 (tp) cc_final: 0.6883 (tp) REVERT: B 376 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6725 (mm-30) REVERT: C 43 ARG cc_start: 0.5494 (ttt90) cc_final: 0.5184 (tpt170) REVERT: C 54 ASP cc_start: 0.6518 (m-30) cc_final: 0.6113 (m-30) REVERT: C 74 LEU cc_start: 0.8170 (tp) cc_final: 0.7913 (tt) REVERT: C 280 HIS cc_start: 0.7817 (t70) cc_final: 0.7321 (t70) REVERT: C 300 LEU cc_start: 0.7590 (tp) cc_final: 0.7149 (mt) REVERT: C 321 LEU cc_start: 0.7299 (tp) cc_final: 0.6897 (tp) REVERT: D 43 ARG cc_start: 0.5485 (ttt90) cc_final: 0.5176 (tpt170) REVERT: D 54 ASP cc_start: 0.6509 (m-30) cc_final: 0.6062 (m-30) REVERT: D 74 LEU cc_start: 0.8187 (tp) cc_final: 0.7933 (tt) REVERT: D 280 HIS cc_start: 0.7810 (t70) cc_final: 0.7286 (t70) REVERT: D 300 LEU cc_start: 0.7589 (tp) cc_final: 0.7150 (mt) REVERT: D 321 LEU cc_start: 0.7308 (tp) cc_final: 0.6911 (tp) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.5387 time to fit residues: 143.1831 Evaluate side-chains 175 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN A 282 GLN A 352 ASN A 409 HIS B 194 GLN B 282 GLN B 352 ASN B 409 HIS C 194 GLN C 282 GLN C 352 ASN C 409 HIS D 194 GLN D 282 GLN D 352 ASN D 409 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108881 restraints weight = 15310.874| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.44 r_work: 0.3027 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15668 Z= 0.195 Angle : 0.640 7.015 21264 Z= 0.337 Chirality : 0.043 0.201 2464 Planarity : 0.005 0.037 2576 Dihedral : 14.189 175.445 2480 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.66 % Allowed : 10.75 % Favored : 86.59 % 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: 2.03 (0.19), residues: 1828 helix: 2.15 (0.15), residues: 1112 sheet: 0.61 (0.35), residues: 252 loop : -0.15 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 298 TYR 0.011 0.002 TYR B 120 PHE 0.017 0.002 PHE A 474 TRP 0.015 0.002 TRP D 491 HIS 0.004 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (15660) covalent geometry : angle 0.63006 / 0.34 (21240) hydrogen bonds : bond 0.06663 / 4.39 ( 1040) hydrogen bonds : angle 4.88820 / 3.49 ( 3276) link_BETA1-4 : bond 0.00180 / 0.09 ( 4) link_BETA1-4 : angle 3.33887 / 1.75 ( 12) link_NAG-ASN : bond 0.00246 / 0.12 ( 4) link_NAG-ASN : angle 3.56114 / 2.06 ( 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 211 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.530 Fit side-chains REVERT: A 74 LEU cc_start: 0.8271 (tp) cc_final: 0.8041 (tt) REVERT: A 115 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7192 (m-30) REVERT: A 176 ASP cc_start: 0.6093 (t0) cc_final: 0.5818 (t0) REVERT: A 300 LEU cc_start: 0.7759 (tp) cc_final: 0.7298 (mt) REVERT: A 321 LEU cc_start: 0.7658 (tp) cc_final: 0.7267 (tp) REVERT: B 74 LEU cc_start: 0.8267 (tp) cc_final: 0.8034 (tt) REVERT: B 115 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7170 (m-30) REVERT: B 176 ASP cc_start: 0.6064 (t0) cc_final: 0.5801 (t0) REVERT: B 253 CYS cc_start: 0.8088 (t) cc_final: 0.7443 (p) REVERT: B 300 LEU cc_start: 0.7719 (tp) cc_final: 0.7238 (mt) REVERT: B 321 LEU cc_start: 0.7654 (tp) cc_final: 0.7268 (tp) REVERT: B 376 GLU cc_start: 0.7240 (mm-30) cc_final: 0.7010 (mm-30) REVERT: C 74 LEU cc_start: 0.8267 (tp) cc_final: 0.8035 (tt) REVERT: C 115 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: C 253 CYS cc_start: 0.8066 (t) cc_final: 0.7440 (p) REVERT: C 300 LEU cc_start: 0.7746 (tp) cc_final: 0.7269 (mt) REVERT: C 321 LEU cc_start: 0.7637 (tp) cc_final: 0.7248 (tp) REVERT: D 54 ASP cc_start: 0.6482 (m-30) cc_final: 0.6257 (m-30) REVERT: D 74 LEU cc_start: 0.8270 (tp) cc_final: 0.8037 (tt) REVERT: D 115 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7211 (m-30) REVERT: D 176 ASP cc_start: 0.6025 (t0) cc_final: 0.5753 (t0) REVERT: D 253 CYS cc_start: 0.8072 (t) cc_final: 0.7437 (p) REVERT: D 300 LEU cc_start: 0.7760 (tp) cc_final: 0.7284 (mt) REVERT: D 321 LEU cc_start: 0.7602 (tp) cc_final: 0.7209 (tp) outliers start: 44 outliers final: 11 residues processed: 191 average time/residue: 0.3923 time to fit residues: 86.3337 Evaluate side-chains 177 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 161 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 74 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 HIS A 282 GLN A 409 HIS B 280 HIS B 282 GLN B 409 HIS C 280 HIS C 282 GLN C 409 HIS D 127 GLN D 280 HIS D 282 GLN D 409 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108383 restraints weight = 15367.626| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.44 r_work: 0.3026 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15668 Z= 0.195 Angle : 0.611 6.622 21264 Z= 0.325 Chirality : 0.043 0.168 2464 Planarity : 0.005 0.041 2576 Dihedral : 13.260 174.838 2480 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.50 % Allowed : 10.63 % Favored : 85.87 % 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: 2.08 (0.19), residues: 1828 helix: 2.20 (0.15), residues: 1108 sheet: 0.73 (0.34), residues: 252 loop : -0.23 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 298 TYR 0.012 0.002 TYR A 120 PHE 0.016 0.002 PHE D 474 TRP 0.016 0.002 TRP B 491 HIS 0.005 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (15660) covalent geometry : angle 0.60145 / 0.32 (21240) hydrogen bonds : bond 0.06708 / 4.42 ( 1040) hydrogen bonds : angle 4.67895 / 3.33 ( 3276) link_BETA1-4 : bond 0.00168 / 0.08 ( 4) link_BETA1-4 : angle 3.18351 / 1.65 ( 12) link_NAG-ASN : bond 0.00215 / 0.11 ( 4) link_NAG-ASN : angle 3.38412 / 1.94 ( 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 226 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 0.382 Fit side-chains REVERT: A 74 LEU cc_start: 0.8218 (tp) cc_final: 0.8001 (tt) REVERT: A 115 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7204 (m-30) REVERT: A 321 LEU cc_start: 0.7625 (tp) cc_final: 0.7265 (tp) REVERT: B 74 LEU cc_start: 0.8225 (tp) cc_final: 0.8009 (tt) REVERT: B 115 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7198 (m-30) REVERT: B 300 LEU cc_start: 0.7770 (tp) cc_final: 0.7568 (mm) REVERT: B 321 LEU cc_start: 0.7632 (tp) cc_final: 0.7275 (tp) REVERT: B 376 GLU cc_start: 0.7236 (mm-30) cc_final: 0.7019 (mm-30) REVERT: C 74 LEU cc_start: 0.8222 (tp) cc_final: 0.8006 (tt) REVERT: C 115 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7196 (m-30) REVERT: C 300 LEU cc_start: 0.7760 (tp) cc_final: 0.7557 (mm) REVERT: C 321 LEU cc_start: 0.7623 (tp) cc_final: 0.7261 (tp) REVERT: D 53 CYS cc_start: 0.6252 (m) cc_final: 0.5963 (m) REVERT: D 54 ASP cc_start: 0.6357 (m-30) cc_final: 0.6120 (m-30) REVERT: D 74 LEU cc_start: 0.8219 (tp) cc_final: 0.8002 (tt) REVERT: D 115 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7214 (m-30) REVERT: D 300 LEU cc_start: 0.7753 (tp) cc_final: 0.7368 (mt) REVERT: D 321 LEU cc_start: 0.7642 (tp) cc_final: 0.7281 (tp) outliers start: 58 outliers final: 20 residues processed: 206 average time/residue: 0.4477 time to fit residues: 104.4567 Evaluate side-chains 190 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 161 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 47 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 HIS A 282 GLN A 352 ASN A 409 HIS B 280 HIS B 282 GLN B 352 ASN B 409 HIS C 280 HIS C 282 GLN C 352 ASN C 409 HIS D 280 HIS D 282 GLN D 352 ASN D 409 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.155303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.109340 restraints weight = 15334.545| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.45 r_work: 0.3041 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15668 Z= 0.165 Angle : 0.564 6.703 21264 Z= 0.299 Chirality : 0.041 0.171 2464 Planarity : 0.005 0.035 2576 Dihedral : 12.633 173.768 2480 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.84 % Allowed : 11.47 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.19), residues: 1828 helix: 2.25 (0.15), residues: 1112 sheet: 0.82 (0.34), residues: 252 loop : -0.17 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 298 TYR 0.010 0.002 TYR A 497 PHE 0.016 0.002 PHE D 474 TRP 0.015 0.002 TRP A 491 HIS 0.004 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (15660) covalent geometry : angle 0.55492 / 0.30 (21240) hydrogen bonds : bond 0.05999 / 3.94 ( 1040) hydrogen bonds : angle 4.47846 / 3.20 ( 3276) link_BETA1-4 : bond 0.00055 / 0.03 ( 4) link_BETA1-4 : angle 2.99563 / 1.55 ( 12) link_NAG-ASN : bond 0.00138 / 0.07 ( 4) link_NAG-ASN : angle 2.98825 / 1.73 ( 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 219 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.648 Fit side-chains REVERT: A 53 CYS cc_start: 0.6288 (m) cc_final: 0.6078 (m) REVERT: A 74 LEU cc_start: 0.8228 (tp) cc_final: 0.8019 (tt) REVERT: A 115 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7286 (m-30) REVERT: A 280 HIS cc_start: 0.8062 (t70) cc_final: 0.7595 (t-170) REVERT: A 300 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7244 (mm) REVERT: A 321 LEU cc_start: 0.7590 (tp) cc_final: 0.7233 (tp) REVERT: B 74 LEU cc_start: 0.8225 (tp) cc_final: 0.8019 (tt) REVERT: B 115 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7269 (m-30) REVERT: B 253 CYS cc_start: 0.8059 (t) cc_final: 0.7430 (p) REVERT: B 280 HIS cc_start: 0.8108 (t70) cc_final: 0.7652 (t-170) REVERT: B 300 LEU cc_start: 0.7759 (tp) cc_final: 0.7381 (mt) REVERT: B 321 LEU cc_start: 0.7600 (tp) cc_final: 0.7244 (tp) REVERT: B 376 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6987 (mp0) REVERT: C 53 CYS cc_start: 0.6297 (m) cc_final: 0.6091 (m) REVERT: C 74 LEU cc_start: 0.8226 (tp) cc_final: 0.8018 (tt) REVERT: C 115 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7292 (m-30) REVERT: C 253 CYS cc_start: 0.7988 (t) cc_final: 0.7395 (p) REVERT: C 300 LEU cc_start: 0.7746 (tp) cc_final: 0.7368 (mt) REVERT: C 321 LEU cc_start: 0.7589 (tp) cc_final: 0.7230 (tp) REVERT: D 53 CYS cc_start: 0.6212 (m) cc_final: 0.5948 (m) REVERT: D 54 ASP cc_start: 0.6390 (m-30) cc_final: 0.6164 (m-30) REVERT: D 74 LEU cc_start: 0.8229 (tp) cc_final: 0.8020 (tt) REVERT: D 115 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7294 (m-30) REVERT: D 253 CYS cc_start: 0.8040 (t) cc_final: 0.7402 (p) REVERT: D 300 LEU cc_start: 0.7748 (tp) cc_final: 0.7373 (mt) REVERT: D 321 LEU cc_start: 0.7610 (tp) cc_final: 0.7253 (tp) outliers start: 47 outliers final: 16 residues processed: 199 average time/residue: 0.5106 time to fit residues: 113.5556 Evaluate side-chains 193 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 161 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 78 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN A 352 ASN B 179 ASN B 352 ASN C 179 ASN C 280 HIS C 282 GLN C 352 ASN D 179 ASN D 280 HIS D 282 GLN D 352 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.153692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107594 restraints weight = 15354.923| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.45 r_work: 0.3016 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15668 Z= 0.226 Angle : 0.656 6.620 21264 Z= 0.343 Chirality : 0.045 0.178 2464 Planarity : 0.006 0.053 2576 Dihedral : 12.734 173.442 2480 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.60 % Allowed : 12.86 % Favored : 84.54 % 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: 1.82 (0.19), residues: 1828 helix: 1.99 (0.15), residues: 1116 sheet: 0.59 (0.33), residues: 252 loop : -0.30 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 338 TYR 0.013 0.003 TYR B 120 PHE 0.019 0.002 PHE C 474 TRP 0.017 0.002 TRP B 491 HIS 0.005 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (15660) covalent geometry : angle 0.64507 / 0.34 (21240) hydrogen bonds : bond 0.06773 / 4.47 ( 1040) hydrogen bonds : angle 4.66049 / 3.32 ( 3276) link_BETA1-4 : bond 0.00318 / 0.16 ( 4) link_BETA1-4 : angle 3.54739 / 1.85 ( 12) link_NAG-ASN : bond 0.00306 / 0.15 ( 4) link_NAG-ASN : angle 3.73207 / 2.13 ( 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 215 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.570 Fit side-chains REVERT: A 53 CYS cc_start: 0.6352 (m) cc_final: 0.6097 (m) REVERT: A 74 LEU cc_start: 0.8264 (tp) cc_final: 0.8048 (tt) REVERT: A 115 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7185 (m-30) REVERT: A 280 HIS cc_start: 0.8126 (t70) cc_final: 0.7713 (t70) REVERT: A 300 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7288 (mm) REVERT: A 321 LEU cc_start: 0.7620 (tp) cc_final: 0.7275 (tp) REVERT: B 74 LEU cc_start: 0.8262 (tp) cc_final: 0.8049 (tt) REVERT: B 115 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: B 252 ASP cc_start: 0.7087 (m-30) cc_final: 0.6865 (m-30) REVERT: B 253 CYS cc_start: 0.8024 (t) cc_final: 0.7446 (p) REVERT: B 280 HIS cc_start: 0.8174 (t70) cc_final: 0.7745 (t70) REVERT: B 300 LEU cc_start: 0.7827 (tp) cc_final: 0.7406 (mt) REVERT: B 321 LEU cc_start: 0.7626 (tp) cc_final: 0.7280 (tp) REVERT: C 53 CYS cc_start: 0.6354 (m) cc_final: 0.6104 (m) REVERT: C 74 LEU cc_start: 0.8262 (tp) cc_final: 0.8047 (tt) REVERT: C 115 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7218 (m-30) REVERT: C 252 ASP cc_start: 0.7082 (m-30) cc_final: 0.6870 (m-30) REVERT: C 253 CYS cc_start: 0.8014 (t) cc_final: 0.7445 (p) REVERT: C 280 HIS cc_start: 0.8152 (t70) cc_final: 0.7702 (t-170) REVERT: C 300 LEU cc_start: 0.7831 (tp) cc_final: 0.7417 (mt) REVERT: C 321 LEU cc_start: 0.7616 (tp) cc_final: 0.7268 (tp) REVERT: D 53 CYS cc_start: 0.6361 (m) cc_final: 0.6073 (m) REVERT: D 54 ASP cc_start: 0.6434 (m-30) cc_final: 0.6136 (m-30) REVERT: D 74 LEU cc_start: 0.8265 (tp) cc_final: 0.8050 (tt) REVERT: D 115 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7212 (m-30) REVERT: D 252 ASP cc_start: 0.7032 (m-30) cc_final: 0.6827 (m-30) REVERT: D 253 CYS cc_start: 0.8017 (t) cc_final: 0.7439 (p) REVERT: D 280 HIS cc_start: 0.8144 (t70) cc_final: 0.7696 (t-170) REVERT: D 300 LEU cc_start: 0.7819 (tp) cc_final: 0.7397 (mt) REVERT: D 321 LEU cc_start: 0.7653 (tp) cc_final: 0.7287 (tp) outliers start: 43 outliers final: 25 residues processed: 197 average time/residue: 0.5343 time to fit residues: 117.9982 Evaluate side-chains 201 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 28 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 ASN A 409 HIS B 282 GLN B 352 ASN B 409 HIS C 352 ASN C 409 HIS D 352 ASN D 409 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.154081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.108142 restraints weight = 15262.250| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.44 r_work: 0.3021 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15668 Z= 0.202 Angle : 0.619 6.758 21264 Z= 0.325 Chirality : 0.044 0.175 2464 Planarity : 0.005 0.046 2576 Dihedral : 12.505 173.598 2480 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.78 % Allowed : 12.86 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 1828 helix: 1.97 (0.15), residues: 1120 sheet: 0.56 (0.33), residues: 252 loop : -0.20 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 298 TYR 0.012 0.002 TYR C 120 PHE 0.018 0.002 PHE A 474 TRP 0.017 0.002 TRP C 491 HIS 0.004 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (15660) covalent geometry : angle 0.60943 / 0.32 (21240) hydrogen bonds : bond 0.06408 / 4.22 ( 1040) hydrogen bonds : angle 4.53323 / 3.23 ( 3276) link_BETA1-4 : bond 0.00233 / 0.12 ( 4) link_BETA1-4 : angle 3.26774 / 1.69 ( 12) link_NAG-ASN : bond 0.00196 / 0.10 ( 4) link_NAG-ASN : angle 3.33847 / 1.91 ( 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 216 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.598 Fit side-chains REVERT: A 53 CYS cc_start: 0.6324 (m) cc_final: 0.6104 (m) REVERT: A 74 LEU cc_start: 0.8270 (tp) cc_final: 0.8057 (tt) REVERT: A 115 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7307 (m-30) REVERT: A 280 HIS cc_start: 0.8141 (t70) cc_final: 0.7809 (t70) REVERT: A 300 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7279 (mm) REVERT: A 321 LEU cc_start: 0.7650 (tp) cc_final: 0.7289 (tp) REVERT: B 74 LEU cc_start: 0.8271 (tp) cc_final: 0.8060 (tt) REVERT: B 115 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7294 (m-30) REVERT: B 252 ASP cc_start: 0.7113 (m-30) cc_final: 0.6877 (m-30) REVERT: B 253 CYS cc_start: 0.8035 (t) cc_final: 0.7437 (p) REVERT: B 280 HIS cc_start: 0.8150 (t70) cc_final: 0.7638 (t-170) REVERT: B 300 LEU cc_start: 0.7817 (tp) cc_final: 0.7391 (mt) REVERT: B 321 LEU cc_start: 0.7658 (tp) cc_final: 0.7297 (tp) REVERT: C 53 CYS cc_start: 0.6336 (m) cc_final: 0.6098 (m) REVERT: C 74 LEU cc_start: 0.8264 (tp) cc_final: 0.8053 (tt) REVERT: C 115 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: C 252 ASP cc_start: 0.7122 (m-30) cc_final: 0.6888 (m-30) REVERT: C 253 CYS cc_start: 0.7998 (t) cc_final: 0.7415 (p) REVERT: C 280 HIS cc_start: 0.8143 (t70) cc_final: 0.7739 (t70) REVERT: C 300 LEU cc_start: 0.7814 (tp) cc_final: 0.7391 (mt) REVERT: C 321 LEU cc_start: 0.7642 (tp) cc_final: 0.7277 (tp) REVERT: D 53 CYS cc_start: 0.6392 (m) cc_final: 0.6098 (m) REVERT: D 54 ASP cc_start: 0.6429 (m-30) cc_final: 0.6132 (m-30) REVERT: D 74 LEU cc_start: 0.8273 (tp) cc_final: 0.8060 (tt) REVERT: D 115 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7328 (m-30) REVERT: D 252 ASP cc_start: 0.7101 (m-30) cc_final: 0.6870 (m-30) REVERT: D 253 CYS cc_start: 0.7993 (t) cc_final: 0.7392 (p) REVERT: D 280 HIS cc_start: 0.8139 (t70) cc_final: 0.7702 (t70) REVERT: D 300 LEU cc_start: 0.7828 (tp) cc_final: 0.7404 (mt) REVERT: D 321 LEU cc_start: 0.7643 (tp) cc_final: 0.7283 (tp) outliers start: 46 outliers final: 28 residues processed: 199 average time/residue: 0.4831 time to fit residues: 108.2060 Evaluate side-chains 200 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 56 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 170 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 ASN A 409 HIS B 282 GLN B 352 ASN B 409 HIS C 282 GLN C 352 ASN C 409 HIS D 282 GLN D 352 ASN D 409 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.111622 restraints weight = 15270.014| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.41 r_work: 0.3062 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15668 Z= 0.146 Angle : 0.538 6.858 21264 Z= 0.284 Chirality : 0.040 0.170 2464 Planarity : 0.004 0.038 2576 Dihedral : 12.035 173.590 2480 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.66 % Allowed : 13.41 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.20), residues: 1828 helix: 2.36 (0.15), residues: 1100 sheet: 0.70 (0.34), residues: 252 loop : -0.21 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 187 TYR 0.011 0.002 TYR B 497 PHE 0.014 0.001 PHE C 474 TRP 0.015 0.002 TRP B 491 HIS 0.004 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (15660) covalent geometry : angle 0.53044 / 0.28 (21240) hydrogen bonds : bond 0.05616 / 3.68 ( 1040) hydrogen bonds : angle 4.31150 / 3.08 ( 3276) link_BETA1-4 : bond 0.00021 / 0.01 ( 4) link_BETA1-4 : angle 2.70579 / 1.38 ( 12) link_NAG-ASN : bond 0.00143 / 0.07 ( 4) link_NAG-ASN : angle 2.71087 / 1.57 ( 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 214 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.627 Fit side-chains REVERT: A 53 CYS cc_start: 0.6343 (m) cc_final: 0.6118 (m) REVERT: A 74 LEU cc_start: 0.8287 (tp) cc_final: 0.8084 (tt) REVERT: A 115 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: A 280 HIS cc_start: 0.8152 (t70) cc_final: 0.7680 (t70) REVERT: A 321 LEU cc_start: 0.7674 (tp) cc_final: 0.7295 (tp) REVERT: B 74 LEU cc_start: 0.8278 (tp) cc_final: 0.8075 (tt) REVERT: B 115 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: B 252 ASP cc_start: 0.7051 (m-30) cc_final: 0.6791 (m-30) REVERT: B 253 CYS cc_start: 0.8038 (t) cc_final: 0.7507 (m) REVERT: B 280 HIS cc_start: 0.8171 (t70) cc_final: 0.7674 (t-170) REVERT: B 300 LEU cc_start: 0.7808 (tp) cc_final: 0.7392 (mt) REVERT: B 321 LEU cc_start: 0.7668 (tp) cc_final: 0.7292 (tp) REVERT: C 53 CYS cc_start: 0.6401 (m) cc_final: 0.6151 (m) REVERT: C 74 LEU cc_start: 0.8273 (tp) cc_final: 0.8071 (tt) REVERT: C 115 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: C 252 ASP cc_start: 0.7062 (m-30) cc_final: 0.6803 (m-30) REVERT: C 253 CYS cc_start: 0.8010 (t) cc_final: 0.7499 (m) REVERT: C 280 HIS cc_start: 0.8152 (t70) cc_final: 0.7678 (t-170) REVERT: C 300 LEU cc_start: 0.7793 (tp) cc_final: 0.7378 (mt) REVERT: C 321 LEU cc_start: 0.7671 (tp) cc_final: 0.7308 (tp) REVERT: D 53 CYS cc_start: 0.6374 (m) cc_final: 0.6068 (m) REVERT: D 54 ASP cc_start: 0.6420 (m-30) cc_final: 0.6144 (m-30) REVERT: D 74 LEU cc_start: 0.8284 (tp) cc_final: 0.8082 (tt) REVERT: D 115 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: D 252 ASP cc_start: 0.7050 (m-30) cc_final: 0.6777 (m-30) REVERT: D 253 CYS cc_start: 0.8018 (t) cc_final: 0.7492 (m) REVERT: D 280 HIS cc_start: 0.8151 (t70) cc_final: 0.7679 (t-170) REVERT: D 300 LEU cc_start: 0.7797 (tp) cc_final: 0.7392 (mt) REVERT: D 321 LEU cc_start: 0.7682 (tp) cc_final: 0.7319 (tp) outliers start: 44 outliers final: 15 residues processed: 196 average time/residue: 0.4961 time to fit residues: 109.1561 Evaluate side-chains 180 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 161 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 60 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 ASN A 409 HIS B 282 GLN B 352 ASN B 409 HIS C 282 GLN C 352 ASN C 409 HIS D 282 GLN D 352 ASN D 409 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.155220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109214 restraints weight = 15316.812| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.45 r_work: 0.3043 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15668 Z= 0.167 Angle : 0.573 6.820 21264 Z= 0.301 Chirality : 0.041 0.172 2464 Planarity : 0.005 0.039 2576 Dihedral : 12.056 173.275 2480 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.17 % Allowed : 14.37 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.19), residues: 1828 helix: 2.23 (0.15), residues: 1112 sheet: 0.73 (0.34), residues: 252 loop : -0.11 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 187 TYR 0.010 0.002 TYR C 497 PHE 0.015 0.002 PHE C 474 TRP 0.014 0.002 TRP D 491 HIS 0.004 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (15660) covalent geometry : angle 0.56451 / 0.30 (21240) hydrogen bonds : bond 0.05914 / 3.89 ( 1040) hydrogen bonds : angle 4.36969 / 3.12 ( 3276) link_BETA1-4 : bond 0.00027 / 0.01 ( 4) link_BETA1-4 : angle 3.00086 / 1.54 ( 12) link_NAG-ASN : bond 0.00145 / 0.07 ( 4) link_NAG-ASN : angle 3.02448 / 1.74 ( 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 198 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.701 Fit side-chains REVERT: A 53 CYS cc_start: 0.6329 (m) cc_final: 0.6104 (m) REVERT: A 74 LEU cc_start: 0.8266 (tp) cc_final: 0.8058 (tt) REVERT: A 115 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: A 280 HIS cc_start: 0.8134 (t70) cc_final: 0.7675 (t70) REVERT: A 321 LEU cc_start: 0.7693 (tp) cc_final: 0.7316 (tp) REVERT: B 74 LEU cc_start: 0.8270 (tp) cc_final: 0.8063 (tt) REVERT: B 115 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: B 252 ASP cc_start: 0.7023 (m-30) cc_final: 0.6772 (m-30) REVERT: B 253 CYS cc_start: 0.8014 (t) cc_final: 0.7467 (m) REVERT: B 280 HIS cc_start: 0.8144 (t70) cc_final: 0.7639 (t-170) REVERT: B 300 LEU cc_start: 0.7784 (tp) cc_final: 0.7371 (mt) REVERT: B 321 LEU cc_start: 0.7694 (tp) cc_final: 0.7321 (tp) REVERT: C 53 CYS cc_start: 0.6359 (m) cc_final: 0.6144 (m) REVERT: C 74 LEU cc_start: 0.8271 (tp) cc_final: 0.8062 (tt) REVERT: C 115 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: C 252 ASP cc_start: 0.7039 (m-30) cc_final: 0.6795 (m-30) REVERT: C 253 CYS cc_start: 0.7974 (t) cc_final: 0.7447 (m) REVERT: C 280 HIS cc_start: 0.8123 (t70) cc_final: 0.7634 (t-170) REVERT: C 298 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6095 (ttt-90) REVERT: C 300 LEU cc_start: 0.7799 (tp) cc_final: 0.7377 (mt) REVERT: C 321 LEU cc_start: 0.7677 (tp) cc_final: 0.7302 (tp) REVERT: D 53 CYS cc_start: 0.6397 (m) cc_final: 0.6094 (m) REVERT: D 54 ASP cc_start: 0.6367 (m-30) cc_final: 0.6103 (m-30) REVERT: D 74 LEU cc_start: 0.8270 (tp) cc_final: 0.8061 (tt) REVERT: D 115 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7329 (m-30) REVERT: D 252 ASP cc_start: 0.7031 (m-30) cc_final: 0.6780 (m-30) REVERT: D 253 CYS cc_start: 0.7993 (t) cc_final: 0.7446 (m) REVERT: D 280 HIS cc_start: 0.8133 (t70) cc_final: 0.7642 (t-170) REVERT: D 300 LEU cc_start: 0.7790 (tp) cc_final: 0.7378 (mt) REVERT: D 321 LEU cc_start: 0.7685 (tp) cc_final: 0.7310 (tp) outliers start: 36 outliers final: 17 residues processed: 186 average time/residue: 0.4917 time to fit residues: 103.1733 Evaluate side-chains 181 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 161 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 180 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 GLN A 352 ASN B 282 GLN B 352 ASN C 282 GLN C 352 ASN D 282 GLN D 352 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.153299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.107191 restraints weight = 15473.731| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.46 r_work: 0.3013 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15668 Z= 0.211 Angle : 0.640 6.794 21264 Z= 0.333 Chirality : 0.044 0.176 2464 Planarity : 0.006 0.050 2576 Dihedral : 12.372 173.544 2480 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.48 % Allowed : 14.19 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.19), residues: 1828 helix: 2.03 (0.15), residues: 1116 sheet: 0.69 (0.34), residues: 252 loop : -0.22 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 338 TYR 0.013 0.002 TYR B 120 PHE 0.017 0.002 PHE C 474 TRP 0.016 0.002 TRP C 491 HIS 0.005 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (15660) covalent geometry : angle 0.63004 / 0.33 (21240) hydrogen bonds : bond 0.06469 / 4.26 ( 1040) hydrogen bonds : angle 4.51638 / 3.22 ( 3276) link_BETA1-4 : bond 0.00213 / 0.11 ( 4) link_BETA1-4 : angle 3.42664 / 1.78 ( 12) link_NAG-ASN : bond 0.00241 / 0.12 ( 4) link_NAG-ASN : angle 3.40465 / 1.94 ( 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 207 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.532 Fit side-chains REVERT: A 53 CYS cc_start: 0.6362 (m) cc_final: 0.6142 (m) REVERT: A 74 LEU cc_start: 0.8252 (tp) cc_final: 0.8047 (tt) REVERT: A 115 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7444 (m-30) REVERT: A 280 HIS cc_start: 0.8141 (t70) cc_final: 0.7590 (t-170) REVERT: A 300 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7173 (mm) REVERT: A 321 LEU cc_start: 0.7611 (tp) cc_final: 0.7262 (tp) REVERT: A 376 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7249 (mp0) REVERT: B 74 LEU cc_start: 0.8244 (tp) cc_final: 0.8034 (tt) REVERT: B 115 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: B 252 ASP cc_start: 0.7032 (m-30) cc_final: 0.6765 (m-30) REVERT: B 253 CYS cc_start: 0.8009 (t) cc_final: 0.7397 (m) REVERT: B 280 HIS cc_start: 0.8181 (t70) cc_final: 0.7655 (t-170) REVERT: B 300 LEU cc_start: 0.7796 (tp) cc_final: 0.7378 (mt) REVERT: B 321 LEU cc_start: 0.7622 (tp) cc_final: 0.7274 (tp) REVERT: B 376 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: C 53 CYS cc_start: 0.6362 (m) cc_final: 0.6145 (m) REVERT: C 74 LEU cc_start: 0.8242 (tp) cc_final: 0.8033 (tt) REVERT: C 115 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7446 (m-30) REVERT: C 252 ASP cc_start: 0.7015 (m-30) cc_final: 0.6743 (m-30) REVERT: C 253 CYS cc_start: 0.7978 (t) cc_final: 0.7376 (m) REVERT: C 280 HIS cc_start: 0.8143 (t70) cc_final: 0.7633 (t-170) REVERT: C 298 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6643 (ttm-80) REVERT: C 300 LEU cc_start: 0.7801 (tp) cc_final: 0.7384 (mt) REVERT: C 321 LEU cc_start: 0.7612 (tp) cc_final: 0.7266 (tp) REVERT: D 53 CYS cc_start: 0.6377 (m) cc_final: 0.6101 (m) REVERT: D 54 ASP cc_start: 0.6496 (m-30) cc_final: 0.6217 (m-30) REVERT: D 74 LEU cc_start: 0.8255 (tp) cc_final: 0.8044 (tt) REVERT: D 252 ASP cc_start: 0.7007 (m-30) cc_final: 0.6737 (m-30) REVERT: D 253 CYS cc_start: 0.7974 (t) cc_final: 0.7355 (m) REVERT: D 280 HIS cc_start: 0.8172 (t70) cc_final: 0.7658 (t-170) REVERT: D 300 LEU cc_start: 0.7810 (tp) cc_final: 0.7398 (mt) REVERT: D 321 LEU cc_start: 0.7615 (tp) cc_final: 0.7268 (tp) outliers start: 41 outliers final: 21 residues processed: 188 average time/residue: 0.5148 time to fit residues: 108.6047 Evaluate side-chains 193 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 27 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 176 optimal weight: 0.0070 chunk 164 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 GLN A 352 ASN A 409 HIS B 282 GLN B 352 ASN B 409 HIS C 282 GLN C 352 ASN C 409 HIS D 282 GLN D 352 ASN D 409 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.108993 restraints weight = 15598.090| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.45 r_work: 0.3041 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15668 Z= 0.148 Angle : 0.550 6.951 21264 Z= 0.289 Chirality : 0.041 0.168 2464 Planarity : 0.004 0.040 2576 Dihedral : 11.991 173.880 2480 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.57 % Allowed : 15.04 % Favored : 83.39 % 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: 2.21 (0.20), residues: 1828 helix: 2.32 (0.15), residues: 1104 sheet: 0.80 (0.35), residues: 252 loop : -0.20 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 187 TYR 0.011 0.002 TYR A 497 PHE 0.014 0.001 PHE C 474 TRP 0.015 0.002 TRP A 491 HIS 0.004 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (15660) covalent geometry : angle 0.54216 / 0.29 (21240) hydrogen bonds : bond 0.05640 / 3.70 ( 1040) hydrogen bonds : angle 4.30832 / 3.08 ( 3276) link_BETA1-4 : bond 0.00020 / 0.01 ( 4) link_BETA1-4 : angle 2.81241 / 1.43 ( 12) link_NAG-ASN : bond 0.00146 / 0.07 ( 4) link_NAG-ASN : angle 2.79015 / 1.61 ( 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 186 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.522 Fit side-chains REVERT: A 53 CYS cc_start: 0.6362 (m) cc_final: 0.6134 (m) REVERT: A 74 LEU cc_start: 0.8281 (tp) cc_final: 0.8077 (tt) REVERT: A 115 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: A 280 HIS cc_start: 0.8138 (t70) cc_final: 0.7586 (t-170) REVERT: A 321 LEU cc_start: 0.7609 (tp) cc_final: 0.7244 (tp) REVERT: B 74 LEU cc_start: 0.8269 (tp) cc_final: 0.8061 (tt) REVERT: B 115 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: B 252 ASP cc_start: 0.6991 (m-30) cc_final: 0.6741 (m-30) REVERT: B 253 CYS cc_start: 0.7993 (t) cc_final: 0.7395 (m) REVERT: B 280 HIS cc_start: 0.8132 (t70) cc_final: 0.7601 (t-170) REVERT: B 300 LEU cc_start: 0.7794 (tp) cc_final: 0.7383 (mt) REVERT: B 321 LEU cc_start: 0.7617 (tp) cc_final: 0.7252 (tp) REVERT: C 53 CYS cc_start: 0.6369 (m) cc_final: 0.6159 (m) REVERT: C 74 LEU cc_start: 0.8269 (tp) cc_final: 0.8063 (tt) REVERT: C 115 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7475 (m-30) REVERT: C 252 ASP cc_start: 0.7001 (m-30) cc_final: 0.6753 (m-30) REVERT: C 253 CYS cc_start: 0.7987 (t) cc_final: 0.7391 (m) REVERT: C 280 HIS cc_start: 0.8123 (t70) cc_final: 0.7599 (t-170) REVERT: C 298 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6167 (ttt-90) REVERT: C 300 LEU cc_start: 0.7783 (tp) cc_final: 0.7369 (mt) REVERT: C 321 LEU cc_start: 0.7593 (tp) cc_final: 0.7240 (tp) REVERT: D 53 CYS cc_start: 0.6399 (m) cc_final: 0.6113 (m) REVERT: D 54 ASP cc_start: 0.6481 (m-30) cc_final: 0.6211 (m-30) REVERT: D 74 LEU cc_start: 0.8273 (tp) cc_final: 0.8066 (tt) REVERT: D 252 ASP cc_start: 0.6996 (m-30) cc_final: 0.6749 (m-30) REVERT: D 253 CYS cc_start: 0.7989 (t) cc_final: 0.7377 (m) REVERT: D 280 HIS cc_start: 0.8160 (t70) cc_final: 0.7636 (t-170) REVERT: D 300 LEU cc_start: 0.7799 (tp) cc_final: 0.7379 (mt) REVERT: D 321 LEU cc_start: 0.7595 (tp) cc_final: 0.7229 (tp) outliers start: 26 outliers final: 10 residues processed: 175 average time/residue: 0.4730 time to fit residues: 93.4883 Evaluate side-chains 173 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 161 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 128 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 180 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 GLN A 352 ASN B 282 GLN B 352 ASN C 282 GLN C 352 ASN D 282 GLN D 352 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.152490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.106502 restraints weight = 15445.561| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.45 r_work: 0.3005 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15668 Z= 0.253 Angle : 0.692 7.269 21264 Z= 0.358 Chirality : 0.047 0.179 2464 Planarity : 0.006 0.059 2576 Dihedral : 12.507 173.675 2480 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.81 % Allowed : 14.73 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.19), residues: 1828 helix: 1.87 (0.15), residues: 1120 sheet: 0.63 (0.33), residues: 252 loop : -0.25 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 338 TYR 0.013 0.003 TYR D 120 PHE 0.019 0.002 PHE C 474 TRP 0.015 0.003 TRP B 491 HIS 0.005 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 (15660) covalent geometry : angle 0.68103 / 0.36 (21240) hydrogen bonds : bond 0.06795 / 4.48 ( 1040) hydrogen bonds : angle 4.59938 / 3.27 ( 3276) link_BETA1-4 : bond 0.00293 / 0.15 ( 4) link_BETA1-4 : angle 3.79308 / 1.99 ( 12) link_NAG-ASN : bond 0.00256 / 0.13 ( 4) link_NAG-ASN : angle 3.60512 / 2.05 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5688.69 seconds wall clock time: 97 minutes 44.94 seconds (5864.94 seconds total)