Starting phenix.real_space_refine on Fri Jul 3 18:04:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sq7_25378/07_2026/7sq7_25378_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sq7_25378/07_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_25378/07_2026/7sq7_25378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sq7_25378/07_2026/7sq7_25378.map" model { file = "/net/cci-nas-00/data/ceres_data/7sq7_25378/07_2026/7sq7_25378_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sq7_25378/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 47 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'EUJ': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 3.30, per 1000 atoms: 0.22 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: 1.27 Conformation dependent library (CDL) restraints added in 598.8 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: 0.45 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: 2.55 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.990 Find NCS groups from input model: 0.350 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.430 ------------------------------------------------------------------------------- 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 : 0.514 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: 0.5265 time to fit residues: 139.8869 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 : 0.561 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.154909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108816 restraints weight = 15314.594| |-----------------------------------------------------------------------------| 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: 0.2910 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1587 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= 0.193 Angle : 0.639 7.219 21264 Z= 0.335 Chirality : 0.043 0.198 2464 Planarity : 0.005 0.039 2576 Dihedral : 14.241 175.697 2480 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.66 % Allowed : 10.69 % Favored : 86.65 % 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: 2.14 (0.15), residues: 1112 sheet: 0.62 (0.35), residues: 252 loop : -0.15 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 0.00418 / 0.19 (15660) covalent geometry : angle 0.62860 / 0.33 (21240) hydrogen bonds : bond 0.06823 / 4.50 ( 1040) hydrogen bonds : angle 4.91122 / 3.50 ( 3276) link_BETA1-4 : bond 0.00110 / 0.05 ( 4) link_BETA1-4 : angle 3.28099 / 1.71 ( 12) link_NAG-ASN : bond 0.00198 / 0.10 ( 4) link_NAG-ASN : angle 3.52691 / 2.04 ( 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 210 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 0.577 Fit side-chains REVERT: A 74 LEU cc_start: 0.8275 (tp) cc_final: 0.8044 (tt) REVERT: A 115 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7173 (m-30) REVERT: A 176 ASP cc_start: 0.6083 (t0) cc_final: 0.5818 (t0) REVERT: A 284 CYS cc_start: 0.6641 (p) cc_final: 0.5948 (m) REVERT: A 300 LEU cc_start: 0.7750 (tp) cc_final: 0.7283 (mt) REVERT: A 321 LEU cc_start: 0.7661 (tp) cc_final: 0.7271 (tp) REVERT: B 74 LEU cc_start: 0.8273 (tp) cc_final: 0.8040 (tt) REVERT: B 115 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.7156 (m-30) REVERT: B 176 ASP cc_start: 0.6074 (t0) cc_final: 0.5815 (t0) REVERT: B 253 CYS cc_start: 0.8075 (t) cc_final: 0.7442 (p) REVERT: B 300 LEU cc_start: 0.7720 (tp) cc_final: 0.7233 (mt) REVERT: B 321 LEU cc_start: 0.7659 (tp) cc_final: 0.7273 (tp) REVERT: B 376 GLU cc_start: 0.7241 (mm-30) cc_final: 0.7025 (mm-30) REVERT: C 74 LEU cc_start: 0.8272 (tp) cc_final: 0.8042 (tt) REVERT: C 115 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7187 (m-30) REVERT: C 253 CYS cc_start: 0.8068 (t) cc_final: 0.7453 (p) REVERT: C 300 LEU cc_start: 0.7748 (tp) cc_final: 0.7267 (mt) REVERT: C 321 LEU cc_start: 0.7639 (tp) cc_final: 0.7251 (tp) REVERT: D 54 ASP cc_start: 0.6487 (m-30) cc_final: 0.6263 (m-30) REVERT: D 74 LEU cc_start: 0.8282 (tp) cc_final: 0.8049 (tt) REVERT: D 115 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: D 253 CYS cc_start: 0.8068 (t) cc_final: 0.7449 (p) REVERT: D 300 LEU cc_start: 0.7654 (tp) cc_final: 0.7275 (mt) REVERT: D 321 LEU cc_start: 0.7660 (tp) cc_final: 0.7271 (tp) outliers start: 44 outliers final: 12 residues processed: 190 average time/residue: 0.3949 time to fit residues: 86.5476 Evaluate side-chains 178 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 66 LEU 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: 8.9990 chunk 101 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.153500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107393 restraints weight = 15391.609| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.44 r_work: 0.3008 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 15668 Z= 0.243 Angle : 0.687 6.931 21264 Z= 0.362 Chirality : 0.046 0.171 2464 Planarity : 0.006 0.054 2576 Dihedral : 13.586 174.350 2480 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.38 % Allowed : 11.29 % Favored : 85.33 % 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: 1.74 (0.19), residues: 1828 helix: 1.89 (0.14), residues: 1116 sheet: 0.59 (0.34), residues: 252 loop : -0.27 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 298 TYR 0.017 0.003 TYR A 120 PHE 0.019 0.003 PHE D 474 TRP 0.018 0.002 TRP B 491 HIS 0.005 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 (15660) covalent geometry : angle 0.67537 / 0.36 (21240) hydrogen bonds : bond 0.07192 / 4.74 ( 1040) hydrogen bonds : angle 4.83791 / 3.45 ( 3276) link_BETA1-4 : bond 0.00433 / 0.22 ( 4) link_BETA1-4 : angle 3.61178 / 1.90 ( 12) link_NAG-ASN : bond 0.00302 / 0.15 ( 4) link_NAG-ASN : angle 4.10618 / 2.34 ( 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: 56 poor density : 170 time to evaluate : 0.455 Fit side-chains REVERT: A 53 CYS cc_start: 0.6246 (m) cc_final: 0.6013 (m) REVERT: A 74 LEU cc_start: 0.8239 (tp) cc_final: 0.8017 (tt) REVERT: A 300 LEU cc_start: 0.7753 (tp) cc_final: 0.7370 (mt) REVERT: A 321 LEU cc_start: 0.7587 (tp) cc_final: 0.7242 (tp) REVERT: B 53 CYS cc_start: 0.6277 (m) cc_final: 0.6069 (m) REVERT: B 74 LEU cc_start: 0.8243 (tp) cc_final: 0.8018 (tt) REVERT: B 300 LEU cc_start: 0.7754 (tp) cc_final: 0.7364 (mt) REVERT: B 321 LEU cc_start: 0.7598 (tp) cc_final: 0.7255 (tp) REVERT: B 376 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6988 (mm-30) REVERT: C 53 CYS cc_start: 0.6036 (m) cc_final: 0.5749 (m) REVERT: C 74 LEU cc_start: 0.8235 (tp) cc_final: 0.8011 (tt) REVERT: C 300 LEU cc_start: 0.7742 (tp) cc_final: 0.7363 (mt) REVERT: C 321 LEU cc_start: 0.7590 (tp) cc_final: 0.7242 (tp) REVERT: D 53 CYS cc_start: 0.6271 (m) cc_final: 0.5974 (m) REVERT: D 54 ASP cc_start: 0.6357 (m-30) cc_final: 0.6017 (m-30) REVERT: D 74 LEU cc_start: 0.8228 (tp) cc_final: 0.8007 (tt) REVERT: D 300 LEU cc_start: 0.7759 (tp) cc_final: 0.7355 (mt) REVERT: D 321 LEU cc_start: 0.7608 (tp) cc_final: 0.7262 (tp) outliers start: 56 outliers final: 24 residues processed: 206 average time/residue: 0.4414 time to fit residues: 102.7807 Evaluate side-chains 195 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 146 ARG Chi-restraints excluded: chain A residue 161 SER 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 47 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.156784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111027 restraints weight = 15369.889| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.45 r_work: 0.3073 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15668 Z= 0.131 Angle : 0.513 6.861 21264 Z= 0.275 Chirality : 0.039 0.171 2464 Planarity : 0.004 0.037 2576 Dihedral : 12.573 174.101 2480 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.69 % Allowed : 12.14 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.20), residues: 1828 helix: 2.34 (0.15), residues: 1112 sheet: 0.71 (0.35), residues: 252 loop : -0.07 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 298 TYR 0.011 0.001 TYR A 497 PHE 0.014 0.001 PHE B 474 TRP 0.013 0.001 TRP A 491 HIS 0.004 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (15660) covalent geometry : angle 0.50727 / 0.27 (21240) hydrogen bonds : bond 0.05466 / 3.59 ( 1040) hydrogen bonds : angle 4.31446 / 3.09 ( 3276) link_BETA1-4 : bond 0.00136 / 0.07 ( 4) link_BETA1-4 : angle 2.45028 / 1.25 ( 12) link_NAG-ASN : bond 0.00141 / 0.07 ( 4) link_NAG-ASN : angle 2.30991 / 1.34 ( 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 199 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.651 Fit side-chains REVERT: A 53 CYS cc_start: 0.6294 (m) cc_final: 0.6055 (m) REVERT: A 74 LEU cc_start: 0.8247 (tp) cc_final: 0.8040 (tt) REVERT: A 95 GLU cc_start: 0.8434 (tt0) cc_final: 0.8223 (mm-30) REVERT: A 187 ARG cc_start: 0.6378 (ttm-80) cc_final: 0.6143 (ttm-80) REVERT: A 280 HIS cc_start: 0.8082 (t70) cc_final: 0.7640 (t-170) REVERT: A 300 LEU cc_start: 0.7754 (tp) cc_final: 0.7385 (mt) REVERT: A 321 LEU cc_start: 0.7581 (tp) cc_final: 0.7211 (OUTLIER) REVERT: B 74 LEU cc_start: 0.8245 (tp) cc_final: 0.8040 (tt) REVERT: B 253 CYS cc_start: 0.8026 (t) cc_final: 0.7392 (p) REVERT: B 280 HIS cc_start: 0.8095 (t70) cc_final: 0.7648 (t-170) REVERT: B 300 LEU cc_start: 0.7752 (tp) cc_final: 0.7375 (mt) REVERT: B 321 LEU cc_start: 0.7599 (tp) cc_final: 0.7231 (OUTLIER) REVERT: B 376 GLU cc_start: 0.7229 (mm-30) cc_final: 0.7025 (mm-30) REVERT: C 74 LEU cc_start: 0.8248 (tp) cc_final: 0.8043 (tt) REVERT: C 95 GLU cc_start: 0.8421 (tt0) cc_final: 0.8215 (mm-30) REVERT: C 253 CYS cc_start: 0.7967 (t) cc_final: 0.7363 (p) REVERT: C 280 HIS cc_start: 0.8102 (t70) cc_final: 0.7638 (t-170) REVERT: C 300 LEU cc_start: 0.7741 (tp) cc_final: 0.7362 (mt) REVERT: C 321 LEU cc_start: 0.7562 (tp) cc_final: 0.7200 (tp) REVERT: D 54 ASP cc_start: 0.6312 (m-30) cc_final: 0.6096 (m-30) REVERT: D 74 LEU cc_start: 0.8241 (tp) cc_final: 0.8035 (tt) REVERT: D 187 ARG cc_start: 0.6336 (ttm-80) cc_final: 0.6102 (ttm-80) REVERT: D 253 CYS cc_start: 0.8008 (t) cc_final: 0.7372 (p) REVERT: D 280 HIS cc_start: 0.8078 (t70) cc_final: 0.7643 (t-170) REVERT: D 300 LEU cc_start: 0.7735 (tp) cc_final: 0.7371 (mt) REVERT: D 321 LEU cc_start: 0.7599 (tp) cc_final: 0.7237 (tp) outliers start: 28 outliers final: 7 residues processed: 189 average time/residue: 0.5228 time to fit residues: 110.0207 Evaluate side-chains 174 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain D residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 78 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 7 optimal weight: 0.4980 chunk 14 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 ASN A 409 HIS B 352 ASN B 409 HIS C 282 GLN 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 = 0.3815 r_free = 0.3815 target = 0.157585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.112066 restraints weight = 15423.486| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.46 r_work: 0.3087 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15668 Z= 0.122 Angle : 0.487 6.691 21264 Z= 0.260 Chirality : 0.039 0.161 2464 Planarity : 0.004 0.039 2576 Dihedral : 12.071 173.740 2480 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.99 % Allowed : 13.29 % Favored : 84.72 % 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: 2.53 (0.20), residues: 1828 helix: 2.62 (0.15), residues: 1088 sheet: 0.86 (0.35), residues: 252 loop : -0.04 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 298 TYR 0.011 0.001 TYR D 497 PHE 0.012 0.001 PHE B 474 TRP 0.011 0.001 TRP A 491 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (15660) covalent geometry : angle 0.48164 / 0.26 (21240) hydrogen bonds : bond 0.05104 / 3.34 ( 1040) hydrogen bonds : angle 4.15138 / 2.97 ( 3276) link_BETA1-4 : bond 0.00139 / 0.07 ( 4) link_BETA1-4 : angle 2.51025 / 1.29 ( 12) link_NAG-ASN : bond 0.00161 / 0.08 ( 4) link_NAG-ASN : angle 1.98846 / 1.15 ( 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 208 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.435 Fit side-chains REVERT: A 74 LEU cc_start: 0.8248 (tp) cc_final: 0.8047 (tt) REVERT: A 252 ASP cc_start: 0.6939 (m-30) cc_final: 0.6693 (m-30) REVERT: A 280 HIS cc_start: 0.8069 (t70) cc_final: 0.7704 (t70) REVERT: A 284 CYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6703 (m) REVERT: A 300 LEU cc_start: 0.7757 (tp) cc_final: 0.7383 (mt) REVERT: A 321 LEU cc_start: 0.7589 (tp) cc_final: 0.7221 (OUTLIER) REVERT: B 253 CYS cc_start: 0.8008 (t) cc_final: 0.7357 (p) REVERT: B 280 HIS cc_start: 0.8095 (t70) cc_final: 0.7695 (t70) REVERT: B 300 LEU cc_start: 0.7799 (tp) cc_final: 0.7399 (mt) REVERT: B 321 LEU cc_start: 0.7605 (tp) cc_final: 0.7239 (OUTLIER) REVERT: C 253 CYS cc_start: 0.7961 (t) cc_final: 0.7330 (p) REVERT: C 280 HIS cc_start: 0.8100 (t70) cc_final: 0.7651 (t-170) REVERT: C 300 LEU cc_start: 0.7778 (tp) cc_final: 0.7390 (mt) REVERT: C 321 LEU cc_start: 0.7593 (tp) cc_final: 0.7225 (OUTLIER) REVERT: D 53 CYS cc_start: 0.6202 (m) cc_final: 0.5918 (m) REVERT: D 253 CYS cc_start: 0.8001 (t) cc_final: 0.7353 (p) REVERT: D 280 HIS cc_start: 0.8086 (t70) cc_final: 0.7709 (t70) REVERT: D 300 LEU cc_start: 0.7795 (tp) cc_final: 0.7407 (mt) REVERT: D 321 LEU cc_start: 0.7602 (tp) cc_final: 0.7232 (OUTLIER) outliers start: 33 outliers final: 14 residues processed: 193 average time/residue: 0.5389 time to fit residues: 115.8571 Evaluate side-chains 185 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain B residue 66 LEU 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 282 GLN 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=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: 10.0000 chunk 136 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 52 optimal weight: 0.0570 chunk 61 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 ASN A 409 HIS B 352 ASN C 352 ASN C 409 HIS D 352 ASN D 409 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108067 restraints weight = 15240.176| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.45 r_work: 0.3019 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15668 Z= 0.220 Angle : 0.640 6.620 21264 Z= 0.334 Chirality : 0.045 0.172 2464 Planarity : 0.006 0.052 2576 Dihedral : 12.493 173.238 2480 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.23 % Allowed : 13.47 % Favored : 84.30 % 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: 2.07 (0.19), residues: 1828 helix: 2.15 (0.15), residues: 1116 sheet: 0.68 (0.34), residues: 252 loop : -0.12 (0.28), residues: 460 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 B 474 TRP 0.014 0.002 TRP A 491 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (15660) covalent geometry : angle 0.62993 / 0.33 (21240) hydrogen bonds : bond 0.06536 / 4.30 ( 1040) hydrogen bonds : angle 4.52789 / 3.23 ( 3276) link_BETA1-4 : bond 0.00176 / 0.09 ( 4) link_BETA1-4 : angle 3.48459 / 1.82 ( 12) link_NAG-ASN : bond 0.00228 / 0.11 ( 4) link_NAG-ASN : angle 3.42537 / 1.95 ( 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 206 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.621 Fit side-chains REVERT: A 74 LEU cc_start: 0.8235 (tp) cc_final: 0.8011 (tt) REVERT: A 115 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: A 280 HIS cc_start: 0.8109 (t70) cc_final: 0.7723 (t70) REVERT: A 300 LEU cc_start: 0.7811 (tp) cc_final: 0.7386 (mt) REVERT: A 314 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7787 (mp) REVERT: A 321 LEU cc_start: 0.7675 (tp) cc_final: 0.7301 (tp) REVERT: B 115 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7343 (m-30) REVERT: B 253 CYS cc_start: 0.8027 (t) cc_final: 0.7414 (p) REVERT: B 280 HIS cc_start: 0.8158 (t70) cc_final: 0.7714 (t70) REVERT: B 300 LEU cc_start: 0.7803 (tp) cc_final: 0.7380 (mt) REVERT: B 314 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7802 (mp) REVERT: B 321 LEU cc_start: 0.7650 (tp) cc_final: 0.7272 (tp) REVERT: B 376 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7173 (mp0) REVERT: C 115 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7341 (m-30) REVERT: C 280 HIS cc_start: 0.8145 (t70) cc_final: 0.7748 (t70) REVERT: C 300 LEU cc_start: 0.7810 (tp) cc_final: 0.7387 (mt) REVERT: C 314 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7799 (mp) REVERT: C 321 LEU cc_start: 0.7647 (tp) cc_final: 0.7264 (tp) REVERT: D 115 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7352 (m-30) REVERT: D 253 CYS cc_start: 0.8003 (t) cc_final: 0.7397 (p) REVERT: D 280 HIS cc_start: 0.8121 (t70) cc_final: 0.7706 (t70) REVERT: D 300 LEU cc_start: 0.7811 (tp) cc_final: 0.7387 (mt) REVERT: D 314 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7773 (mp) REVERT: D 321 LEU cc_start: 0.7652 (tp) cc_final: 0.7273 (tp) outliers start: 37 outliers final: 19 residues processed: 190 average time/residue: 0.5458 time to fit residues: 115.7920 Evaluate side-chains 192 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 A residue 314 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 116 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 314 LEU 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 314 LEU 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 Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 413 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 56 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN A 352 ASN A 409 HIS B 179 ASN B 282 GLN B 352 ASN B 409 HIS C 179 ASN C 352 ASN C 409 HIS D 179 ASN D 282 GLN D 352 ASN D 409 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.154494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110031 restraints weight = 15274.971| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.39 r_work: 0.3023 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 15668 Z= 0.208 Angle : 0.623 6.765 21264 Z= 0.327 Chirality : 0.044 0.173 2464 Planarity : 0.006 0.046 2576 Dihedral : 12.418 173.920 2480 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.78 % Allowed : 13.29 % 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: 1.92 (0.19), residues: 1828 helix: 2.00 (0.15), residues: 1120 sheet: 0.69 (0.34), residues: 252 loop : -0.13 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 298 TYR 0.012 0.002 TYR C 120 PHE 0.018 0.002 PHE B 474 TRP 0.015 0.002 TRP B 491 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (15660) covalent geometry : angle 0.61432 / 0.33 (21240) hydrogen bonds : bond 0.06390 / 4.21 ( 1040) hydrogen bonds : angle 4.50211 / 3.21 ( 3276) link_BETA1-4 : bond 0.00198 / 0.10 ( 4) link_BETA1-4 : angle 3.28955 / 1.70 ( 12) link_NAG-ASN : bond 0.00189 / 0.09 ( 4) link_NAG-ASN : angle 3.12081 / 1.78 ( 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 207 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.500 Fit side-chains REVERT: A 74 LEU cc_start: 0.8258 (tp) cc_final: 0.8051 (tt) REVERT: A 115 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7309 (m-30) REVERT: A 280 HIS cc_start: 0.8149 (t70) cc_final: 0.7709 (t70) REVERT: A 300 LEU cc_start: 0.7804 (tp) cc_final: 0.7391 (mt) REVERT: A 321 LEU cc_start: 0.7688 (tp) cc_final: 0.7323 (tp) REVERT: B 74 LEU cc_start: 0.8299 (tp) cc_final: 0.8090 (tt) REVERT: B 115 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: B 253 CYS cc_start: 0.8018 (t) cc_final: 0.7479 (m) REVERT: B 300 LEU cc_start: 0.7822 (tp) cc_final: 0.7399 (mt) REVERT: B 321 LEU cc_start: 0.7687 (tp) cc_final: 0.7322 (tp) REVERT: C 74 LEU cc_start: 0.8289 (tp) cc_final: 0.8083 (tt) REVERT: C 115 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7318 (m-30) REVERT: C 253 CYS cc_start: 0.7981 (t) cc_final: 0.7430 (m) REVERT: C 280 HIS cc_start: 0.8178 (t70) cc_final: 0.7728 (t70) REVERT: C 300 LEU cc_start: 0.7812 (tp) cc_final: 0.7397 (mt) REVERT: C 321 LEU cc_start: 0.7680 (tp) cc_final: 0.7315 (tp) REVERT: C 376 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: D 74 LEU cc_start: 0.8306 (tp) cc_final: 0.8094 (tt) REVERT: D 115 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: D 253 CYS cc_start: 0.8017 (t) cc_final: 0.7471 (m) REVERT: D 300 LEU cc_start: 0.7811 (tp) cc_final: 0.7397 (mt) REVERT: D 321 LEU cc_start: 0.7686 (tp) cc_final: 0.7323 (tp) outliers start: 46 outliers final: 21 residues processed: 192 average time/residue: 0.4645 time to fit residues: 100.2220 Evaluate side-chains 184 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 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 B residue 510 LEU 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 376 GLU 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 161 SER Chi-restraints excluded: chain D residue 413 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 60 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 98 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 ASN A 409 HIS B 282 GLN B 352 ASN C 352 ASN D 282 GLN D 352 ASN D 409 HIS 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 = 0.153048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107967 restraints weight = 15653.167| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.44 r_work: 0.3017 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15668 Z= 0.229 Angle : 0.666 6.776 21264 Z= 0.347 Chirality : 0.046 0.181 2464 Planarity : 0.006 0.054 2576 Dihedral : 12.601 173.873 2480 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.48 % Allowed : 14.01 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.19), residues: 1828 helix: 1.86 (0.15), residues: 1116 sheet: 0.65 (0.34), residues: 252 loop : -0.36 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 338 TYR 0.013 0.002 TYR C 120 PHE 0.018 0.002 PHE C 474 TRP 0.016 0.002 TRP A 491 HIS 0.005 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (15660) covalent geometry : angle 0.65566 / 0.34 (21240) hydrogen bonds : bond 0.06679 / 4.41 ( 1040) hydrogen bonds : angle 4.59174 / 3.27 ( 3276) link_BETA1-4 : bond 0.00328 / 0.16 ( 4) link_BETA1-4 : angle 3.63581 / 1.90 ( 12) link_NAG-ASN : bond 0.00226 / 0.11 ( 4) link_NAG-ASN : angle 3.55380 / 2.02 ( 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 199 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.474 Fit side-chains REVERT: A 74 LEU cc_start: 0.8274 (tp) cc_final: 0.8056 (tt) REVERT: A 115 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7401 (m-30) REVERT: A 280 HIS cc_start: 0.8139 (t70) cc_final: 0.7666 (t70) REVERT: A 300 LEU cc_start: 0.7822 (tp) cc_final: 0.7380 (mt) REVERT: A 314 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7756 (mp) REVERT: A 321 LEU cc_start: 0.7648 (tp) cc_final: 0.7296 (tp) REVERT: B 74 LEU cc_start: 0.8306 (tp) cc_final: 0.8093 (tt) REVERT: B 115 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7386 (m-30) REVERT: B 253 CYS cc_start: 0.8004 (t) cc_final: 0.7412 (m) REVERT: B 300 LEU cc_start: 0.7807 (tp) cc_final: 0.7378 (mt) REVERT: B 314 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7767 (mp) REVERT: B 321 LEU cc_start: 0.7653 (tp) cc_final: 0.7302 (tp) REVERT: C 74 LEU cc_start: 0.8290 (tp) cc_final: 0.8081 (tt) REVERT: C 115 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7380 (m-30) REVERT: C 253 CYS cc_start: 0.7979 (t) cc_final: 0.7383 (m) REVERT: C 280 HIS cc_start: 0.8174 (t70) cc_final: 0.7833 (t70) REVERT: C 300 LEU cc_start: 0.7814 (tp) cc_final: 0.7389 (mt) REVERT: C 314 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7765 (mp) REVERT: C 321 LEU cc_start: 0.7649 (tp) cc_final: 0.7297 (tp) REVERT: C 376 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: D 74 LEU cc_start: 0.8313 (tp) cc_final: 0.8103 (tt) REVERT: D 115 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: D 253 CYS cc_start: 0.7996 (t) cc_final: 0.7409 (m) REVERT: D 300 LEU cc_start: 0.7804 (tp) cc_final: 0.7379 (mt) REVERT: D 314 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7749 (mp) REVERT: D 321 LEU cc_start: 0.7645 (tp) cc_final: 0.7296 (tp) outliers start: 41 outliers final: 20 residues processed: 181 average time/residue: 0.4458 time to fit residues: 91.0134 Evaluate side-chains 187 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 161 SER Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 314 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 314 LEU 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 314 LEU Chi-restraints excluded: chain C residue 376 GLU 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 161 SER Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 180 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 179 optimal weight: 0.0370 chunk 177 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.5862 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.155874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.110166 restraints weight = 15481.135| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.44 r_work: 0.3058 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15668 Z= 0.132 Angle : 0.519 7.035 21264 Z= 0.276 Chirality : 0.040 0.167 2464 Planarity : 0.004 0.041 2576 Dihedral : 12.042 174.083 2480 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.99 % Allowed : 14.49 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.20), residues: 1828 helix: 2.37 (0.15), residues: 1100 sheet: 0.85 (0.35), residues: 252 loop : -0.22 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 187 TYR 0.012 0.001 TYR A 497 PHE 0.013 0.001 PHE B 474 TRP 0.014 0.001 TRP A 491 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (15660) covalent geometry : angle 0.51283 / 0.27 (21240) hydrogen bonds : bond 0.05314 / 3.48 ( 1040) hydrogen bonds : angle 4.23705 / 3.03 ( 3276) link_BETA1-4 : bond 0.00050 / 0.02 ( 4) link_BETA1-4 : angle 2.60914 / 1.33 ( 12) link_NAG-ASN : bond 0.00137 / 0.07 ( 4) link_NAG-ASN : angle 2.37614 / 1.37 ( 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 185 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.598 Fit side-chains REVERT: A 115 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: A 280 HIS cc_start: 0.8139 (t70) cc_final: 0.7667 (t70) REVERT: A 300 LEU cc_start: 0.7776 (tp) cc_final: 0.7370 (mt) REVERT: A 321 LEU cc_start: 0.7623 (tp) cc_final: 0.7266 (tp) REVERT: A 376 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7295 (mp0) REVERT: B 74 LEU cc_start: 0.8305 (tp) cc_final: 0.8096 (tt) REVERT: B 115 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: B 253 CYS cc_start: 0.7961 (t) cc_final: 0.7365 (m) REVERT: B 300 LEU cc_start: 0.7788 (tp) cc_final: 0.7358 (mt) REVERT: B 321 LEU cc_start: 0.7627 (tp) cc_final: 0.7271 (tp) REVERT: C 74 LEU cc_start: 0.8287 (tp) cc_final: 0.8082 (tt) REVERT: C 115 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: C 253 CYS cc_start: 0.7949 (t) cc_final: 0.7343 (m) REVERT: C 300 LEU cc_start: 0.7787 (tp) cc_final: 0.7381 (mt) REVERT: C 321 LEU cc_start: 0.7619 (tp) cc_final: 0.7263 (tp) REVERT: D 74 LEU cc_start: 0.8321 (tp) cc_final: 0.8116 (tt) REVERT: D 115 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: D 253 CYS cc_start: 0.7980 (t) cc_final: 0.7365 (m) REVERT: D 300 LEU cc_start: 0.7780 (tp) cc_final: 0.7371 (mt) REVERT: D 314 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7776 (mp) REVERT: D 321 LEU cc_start: 0.7618 (tp) cc_final: 0.7260 (tp) outliers start: 33 outliers final: 12 residues processed: 177 average time/residue: 0.4806 time to fit residues: 95.7129 Evaluate side-chains 160 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain D residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 27 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 176 optimal weight: 0.0770 chunk 164 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.7944 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.154395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109391 restraints weight = 15637.615| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.44 r_work: 0.3044 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2615 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= 0.167 Angle : 0.579 6.874 21264 Z= 0.304 Chirality : 0.042 0.172 2464 Planarity : 0.005 0.044 2576 Dihedral : 12.206 173.636 2480 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.69 % Allowed : 14.79 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.20), residues: 1828 helix: 2.22 (0.15), residues: 1112 sheet: 0.81 (0.35), residues: 252 loop : -0.16 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 298 TYR 0.011 0.002 TYR A 497 PHE 0.015 0.002 PHE D 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 0.00369 / 0.17 (15660) covalent geometry : angle 0.57075 / 0.30 (21240) hydrogen bonds : bond 0.05859 / 3.85 ( 1040) hydrogen bonds : angle 4.34962 / 3.10 ( 3276) link_BETA1-4 : bond 0.00071 / 0.04 ( 4) link_BETA1-4 : angle 3.06981 / 1.58 ( 12) link_NAG-ASN : bond 0.00110 / 0.05 ( 4) link_NAG-ASN : angle 2.94464 / 1.69 ( 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 183 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.604 Fit side-chains REVERT: A 115 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: A 280 HIS cc_start: 0.8134 (t70) cc_final: 0.7608 (t-170) REVERT: A 300 LEU cc_start: 0.7799 (tp) cc_final: 0.7375 (mt) REVERT: A 321 LEU cc_start: 0.7670 (tp) cc_final: 0.7303 (tp) REVERT: A 376 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7274 (mp0) REVERT: B 74 LEU cc_start: 0.8282 (tp) cc_final: 0.8073 (tt) REVERT: B 115 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: B 253 CYS cc_start: 0.8007 (t) cc_final: 0.7402 (m) REVERT: B 280 HIS cc_start: 0.8162 (t70) cc_final: 0.7588 (t-170) REVERT: B 300 LEU cc_start: 0.7804 (tp) cc_final: 0.7375 (mt) REVERT: B 321 LEU cc_start: 0.7673 (tp) cc_final: 0.7308 (tp) REVERT: C 74 LEU cc_start: 0.8292 (tp) cc_final: 0.8086 (tt) REVERT: C 115 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: C 253 CYS cc_start: 0.7992 (t) cc_final: 0.7399 (m) REVERT: C 280 HIS cc_start: 0.8179 (t70) cc_final: 0.7603 (t-170) REVERT: C 300 LEU cc_start: 0.7787 (tp) cc_final: 0.7383 (mt) REVERT: C 321 LEU cc_start: 0.7633 (tp) cc_final: 0.7262 (tp) REVERT: D 74 LEU cc_start: 0.8299 (tp) cc_final: 0.8092 (tt) REVERT: D 115 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: D 253 CYS cc_start: 0.8014 (t) cc_final: 0.7413 (m) REVERT: D 280 HIS cc_start: 0.8180 (t70) cc_final: 0.7619 (t-170) REVERT: D 300 LEU cc_start: 0.7790 (tp) cc_final: 0.7376 (mt) REVERT: D 314 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7782 (mp) REVERT: D 321 LEU cc_start: 0.7634 (tp) cc_final: 0.7264 (tp) outliers start: 28 outliers final: 15 residues processed: 171 average time/residue: 0.4720 time to fit residues: 90.7507 Evaluate side-chains 176 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 A residue 413 ILE Chi-restraints excluded: chain B residue 66 LEU 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 C residue 413 ILE 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 Chi-restraints excluded: chain D residue 314 LEU 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 128 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 180 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 171 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 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 = 0.3762 r_free = 0.3762 target = 0.152890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.107960 restraints weight = 15461.014| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.43 r_work: 0.3019 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2604 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= 0.240 Angle : 0.681 7.053 21264 Z= 0.354 Chirality : 0.046 0.178 2464 Planarity : 0.006 0.057 2576 Dihedral : 12.523 173.648 2480 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.93 % Allowed : 14.67 % 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: 1.77 (0.19), residues: 1828 helix: 1.92 (0.15), residues: 1116 sheet: 0.66 (0.34), residues: 252 loop : -0.33 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 338 TYR 0.014 0.003 TYR A 120 PHE 0.019 0.002 PHE D 474 TRP 0.015 0.002 TRP D 491 HIS 0.005 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (15660) covalent geometry : angle 0.67078 / 0.35 (21240) hydrogen bonds : bond 0.06695 / 4.41 ( 1040) hydrogen bonds : angle 4.57622 / 3.26 ( 3276) link_BETA1-4 : bond 0.00324 / 0.16 ( 4) link_BETA1-4 : angle 3.69095 / 1.93 ( 12) link_NAG-ASN : bond 0.00195 / 0.10 ( 4) link_NAG-ASN : angle 3.39562 / 1.92 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5590.25 seconds wall clock time: 96 minutes 0.50 seconds (5760.50 seconds total)