Starting phenix.real_space_refine on Fri Jul 3 21:12:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sq9_25380/07_2026/7sq9_25380_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sq9_25380/07_2026/7sq9_25380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sq9_25380/07_2026/7sq9_25380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sq9_25380/07_2026/7sq9_25380.map" model { file = "/net/cci-nas-00/data/ceres_data/7sq9_25380/07_2026/7sq9_25380_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sq9_25380/07_2026/7sq9_25380_trim.cif" } resolution = 2.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 96 5.16 5 Na 2 4.78 5 C 10352 2.51 5 N 2556 2.21 5 O 2792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 15810 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3800 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 14, 'TRANS': 454} Chain breaks: 2 Chain: "B" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3800 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 14, 'TRANS': 454} Chain breaks: 2 Chain: "C" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3800 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 14, 'TRANS': 454} Chain breaks: 2 Chain: "D" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3800 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 14, 'TRANS': 454} 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: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'A4I': 1, 'EUJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 120 Unusual residues: {'A4I': 1, 'EUJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 120 Unusual residues: {'A4I': 1, 'EUJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 120 Unusual residues: {'A4I': 1, 'EUJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 3.39, per 1000 atoms: 0.21 Number of scatterers: 15810 At special positions: 0 Unit cell: (110.39, 110.39, 109.56, 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 2 11.00 O 2792 8.00 N 2556 7.00 C 10352 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: 1.16 Conformation dependent library (CDL) restraints added in 573.2 milliseconds 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 67.4% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 4.286A pdb=" N LYS A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.891A pdb=" N MET A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 138 Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.501A pdb=" N ILE A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 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 242 through 248 Processing helix chain 'A' and resid 298 through 338 removed outlier: 3.512A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 352 through 377 removed outlier: 3.838A pdb=" N ILE A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.865A pdb=" N VAL A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 408 through 411 Processing helix chain 'A' and resid 412 through 448 Proline residue: A 423 - end of helix removed outlier: 3.840A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.697A pdb=" N ARG A 455 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 469 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.819A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 508 Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'B' and resid 42 through 49 removed outlier: 4.286A pdb=" N LYS B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.892A pdb=" N MET B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 138 Processing helix chain 'B' and resid 138 through 143 removed outlier: 3.502A pdb=" N ILE B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 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 242 through 248 Processing helix chain 'B' and resid 298 through 338 removed outlier: 3.511A pdb=" N VAL B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 352 through 377 removed outlier: 3.838A pdb=" N ILE B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.865A pdb=" N VAL B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 408 through 411 Processing helix chain 'B' and resid 412 through 448 Proline residue: B 423 - end of helix removed outlier: 3.839A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.697A pdb=" N ARG B 455 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 469 Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.819A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 508 Processing helix chain 'B' and resid 508 through 525 Processing helix chain 'C' and resid 42 through 49 removed outlier: 4.287A pdb=" N LYS C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 59 Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.891A pdb=" N MET C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 138 Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.502A pdb=" N ILE C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 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 242 through 248 Processing helix chain 'C' and resid 298 through 338 removed outlier: 3.512A pdb=" N VAL C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 352 through 377 removed outlier: 3.837A pdb=" N ILE C 356 " --> pdb=" O ASN C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.866A pdb=" N VAL C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 Processing helix chain 'C' and resid 408 through 411 Processing helix chain 'C' and resid 412 through 448 Proline residue: C 423 - end of helix removed outlier: 3.841A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 434 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 removed outlier: 3.697A pdb=" N ARG C 455 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 469 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.820A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 508 Processing helix chain 'C' and resid 508 through 525 Processing helix chain 'D' and resid 42 through 49 removed outlier: 4.286A pdb=" N LYS D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 59 Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.891A pdb=" N MET D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 Processing helix chain 'D' and resid 138 through 143 removed outlier: 3.502A pdb=" N ILE D 142 " --> pdb=" O ILE D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 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 242 through 248 Processing helix chain 'D' and resid 298 through 338 removed outlier: 3.511A pdb=" N VAL D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 352 through 377 removed outlier: 3.838A pdb=" N ILE D 356 " --> pdb=" O ASN D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.865A pdb=" N VAL D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 408 through 411 Processing helix chain 'D' and resid 412 through 448 Proline residue: D 423 - end of helix removed outlier: 3.840A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL D 434 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 removed outlier: 3.697A pdb=" N ARG D 455 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 469 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.820A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 508 Processing helix chain 'D' and resid 508 through 525 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 6.802A pdb=" N ARG A 168 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL A 231 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS A 166 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE A 233 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA A 164 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ARG A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLY A 173 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASP A 185 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.801A pdb=" N ARG B 168 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B 231 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N CYS B 166 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 233 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA B 164 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLY B 173 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASP B 185 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 119 removed outlier: 6.802A pdb=" N ARG C 168 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL C 231 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS C 166 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE C 233 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA C 164 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ARG C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLY C 173 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASP C 185 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 119 removed outlier: 6.802A pdb=" N ARG D 168 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL D 231 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS D 166 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE D 233 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA D 164 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLY D 173 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASP D 185 " --> pdb=" O GLY D 173 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 3180 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: 2.14 Time building geometry restraints manager: 1.48 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: 2445 1.32 - 1.44: 4639 1.44 - 1.57: 8928 1.57 - 1.69: 36 1.69 - 1.81: 132 Bond restraints: 16180 Sorted by residual: bond pdb=" C12 A4I D 602 " pdb=" C14 A4I D 602 " ideal model delta sigma weight residual 1.542 1.399 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" C12 A4I C 602 " pdb=" C14 A4I C 602 " ideal model delta sigma weight residual 1.542 1.399 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C33 A4I D 602 " pdb=" C35 A4I D 602 " ideal model delta sigma weight residual 1.534 1.392 0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C33 A4I A 602 " pdb=" C35 A4I A 602 " ideal model delta sigma weight residual 1.534 1.392 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C12 A4I B 602 " pdb=" C14 A4I B 602 " ideal model delta sigma weight residual 1.542 1.400 0.142 2.00e-02 2.50e+03 5.03e+01 ... (remaining 16175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 21404 2.54 - 5.09: 420 5.09 - 7.63: 96 7.63 - 10.17: 36 10.17 - 12.72: 12 Bond angle restraints: 21968 Sorted by residual: angle pdb=" N ARG C 42 " pdb=" CA ARG C 42 " pdb=" C ARG C 42 " ideal model delta sigma weight residual 111.74 117.63 -5.89 1.35e+00 5.49e-01 1.90e+01 angle pdb=" N ARG D 42 " pdb=" CA ARG D 42 " pdb=" C ARG D 42 " ideal model delta sigma weight residual 111.74 117.62 -5.88 1.35e+00 5.49e-01 1.90e+01 angle pdb=" N ARG B 42 " pdb=" CA ARG B 42 " pdb=" C ARG B 42 " ideal model delta sigma weight residual 111.74 117.62 -5.88 1.35e+00 5.49e-01 1.90e+01 angle pdb=" N ARG A 42 " pdb=" CA ARG A 42 " pdb=" C ARG A 42 " ideal model delta sigma weight residual 111.74 117.61 -5.87 1.35e+00 5.49e-01 1.89e+01 angle pdb=" O11 EUJ A 601 " pdb=" P1 EUJ A 601 " pdb=" O12 EUJ A 601 " ideal model delta sigma weight residual 121.88 109.16 12.72 3.00e+00 1.11e-01 1.80e+01 ... (remaining 21963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.72: 9568 31.72 - 63.43: 432 63.43 - 95.15: 60 95.15 - 126.86: 16 126.86 - 158.58: 4 Dihedral angle restraints: 10080 sinusoidal: 4572 harmonic: 5508 Sorted by residual: 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 26.03 158.58 1 3.00e+01 1.11e-03 2.06e+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 26.04 158.57 1 3.00e+01 1.11e-03 2.06e+01 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 26.05 158.56 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 10077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2313 0.090 - 0.180: 183 0.180 - 0.271: 32 0.271 - 0.361: 12 0.361 - 0.451: 12 Chirality restraints: 2552 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 -2.61 0.45 2.00e-01 2.50e+01 5.08e+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 -2.61 0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" C2C EUJ D 601 " pdb=" C1C EUJ D 601 " pdb=" C3C EUJ D 601 " pdb=" O2C EUJ D 601 " both_signs ideal model delta sigma weight residual False -2.16 -2.61 0.45 2.00e-01 2.50e+01 5.05e+00 ... (remaining 2549 not shown) Planarity restraints: 2660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 62 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO C 63 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 63 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 63 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 62 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO A 63 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 63 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 63 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 62 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 63 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 63 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 63 " 0.026 5.00e-02 4.00e+02 ... (remaining 2657 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2531 2.76 - 3.29: 15589 3.29 - 3.83: 27748 3.83 - 4.36: 32764 4.36 - 4.90: 55196 Nonbonded interactions: 133828 Sorted by model distance: nonbonded pdb=" OH TYR C 109 " pdb=" OD1 ASP C 114 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR D 109 " pdb=" OD1 ASP D 114 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR A 109 " pdb=" OD1 ASP A 114 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR B 109 " pdb=" OD1 ASP B 114 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP A 134 " pdb=" OH TYR A 218 " model vdw 2.245 3.040 ... (remaining 133823 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 602) 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.580 Find NCS groups from input model: 0.250 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:5.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 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 0.143 16188 Z= 0.499 Angle : 0.965 12.715 21992 Z= 0.465 Chirality : 0.063 0.451 2552 Planarity : 0.005 0.046 2656 Dihedral : 18.474 158.580 6528 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.19), residues: 1852 helix: 1.79 (0.15), residues: 1104 sheet: 1.27 (0.31), residues: 252 loop : -0.41 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 151 TYR 0.016 0.002 TYR C 497 PHE 0.015 0.002 PHE C 505 TRP 0.009 0.001 TRP B 491 HIS 0.005 0.001 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00949 / 0.50 (16180) covalent geometry : angle 0.96170 / 0.46 (21968) hydrogen bonds : bond 0.11525 / 7.54 ( 1032) hydrogen bonds : angle 6.47218 / 4.63 ( 3180) link_BETA1-4 : bond 0.00622 / 0.31 ( 4) link_BETA1-4 : angle 2.27123 / 1.19 ( 12) link_NAG-ASN : bond 0.00162 / 0.08 ( 4) link_NAG-ASN : angle 3.08961 / 1.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.490 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.7552 time to fit residues: 123.9135 Evaluate side-chains 122 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 469 ASN B 469 ASN C 327 GLN C 469 ASN D 327 GLN D 469 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.149817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110620 restraints weight = 14608.973| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.16 r_work: 0.3156 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16188 Z= 0.130 Angle : 0.593 9.395 21992 Z= 0.291 Chirality : 0.041 0.178 2552 Planarity : 0.004 0.036 2656 Dihedral : 14.414 175.016 3028 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.13 % Allowed : 13.33 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.20), residues: 1852 helix: 2.10 (0.16), residues: 1116 sheet: 0.80 (0.32), residues: 256 loop : 0.26 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 151 TYR 0.013 0.001 TYR C 497 PHE 0.013 0.001 PHE B 235 TRP 0.006 0.001 TRP B 345 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (16180) covalent geometry : angle 0.58945 / 0.29 (21968) hydrogen bonds : bond 0.05223 / 3.47 ( 1032) hydrogen bonds : angle 4.91239 / 3.52 ( 3180) link_BETA1-4 : bond 0.00192 / 0.10 ( 4) link_BETA1-4 : angle 2.24415 / 1.15 ( 12) link_NAG-ASN : bond 0.00282 / 0.14 ( 4) link_NAG-ASN : angle 1.67932 / 0.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.498 Fit side-chains REVERT: A 247 ASN cc_start: 0.8466 (t0) cc_final: 0.8154 (m110) REVERT: A 322 ARG cc_start: 0.6240 (mmm-85) cc_final: 0.5589 (ttm-80) REVERT: B 247 ASN cc_start: 0.8440 (t0) cc_final: 0.8143 (m110) REVERT: C 247 ASN cc_start: 0.8406 (t0) cc_final: 0.8120 (m110) REVERT: C 322 ARG cc_start: 0.6263 (mmm-85) cc_final: 0.5443 (ttm-80) REVERT: D 247 ASN cc_start: 0.8457 (t0) cc_final: 0.8172 (m110) outliers start: 19 outliers final: 4 residues processed: 145 average time/residue: 0.6585 time to fit residues: 104.2331 Evaluate side-chains 132 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain D residue 67 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 140 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 11 optimal weight: 0.0270 chunk 170 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 overall best weight: 2.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS A 327 GLN B 327 GLN C 234 HIS D 234 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107317 restraints weight = 14553.032| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.16 r_work: 0.3104 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16188 Z= 0.174 Angle : 0.606 6.250 21992 Z= 0.314 Chirality : 0.043 0.136 2552 Planarity : 0.005 0.037 2656 Dihedral : 12.015 174.571 3028 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.73 % Allowed : 12.80 % Favored : 85.48 % 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: 1.96 (0.20), residues: 1852 helix: 2.01 (0.15), residues: 1104 sheet: 0.82 (0.32), residues: 260 loop : -0.00 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 151 TYR 0.015 0.002 TYR B 404 PHE 0.017 0.002 PHE D 235 TRP 0.008 0.001 TRP C 491 HIS 0.006 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (16180) covalent geometry : angle 0.59966 / 0.31 (21968) hydrogen bonds : bond 0.06244 / 4.15 ( 1032) hydrogen bonds : angle 5.06848 / 3.62 ( 3180) link_BETA1-4 : bond 0.00250 / 0.12 ( 4) link_BETA1-4 : angle 2.64466 / 1.35 ( 12) link_NAG-ASN : bond 0.00337 / 0.17 ( 4) link_NAG-ASN : angle 2.79990 / 1.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6260 (mmm-85) cc_final: 0.5637 (mtp85) REVERT: A 326 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6385 (mt) REVERT: B 285 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7453 (mttp) REVERT: B 322 ARG cc_start: 0.6213 (mmm-85) cc_final: 0.5858 (mtp85) REVERT: B 326 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6398 (mt) REVERT: C 285 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7442 (mttp) REVERT: C 322 ARG cc_start: 0.6165 (mmm-85) cc_final: 0.5415 (ttm-80) REVERT: C 326 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6387 (mt) REVERT: D 285 LYS cc_start: 0.7712 (mtmm) cc_final: 0.7437 (mttp) REVERT: D 322 ARG cc_start: 0.6190 (mmm-85) cc_final: 0.5835 (mtp85) REVERT: D 326 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6405 (mt) outliers start: 29 outliers final: 21 residues processed: 152 average time/residue: 0.5973 time to fit residues: 99.5054 Evaluate side-chains 137 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 425 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 12 optimal weight: 0.0170 chunk 166 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.149970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110989 restraints weight = 14686.810| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.15 r_work: 0.3161 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16188 Z= 0.116 Angle : 0.503 6.058 21992 Z= 0.261 Chirality : 0.040 0.131 2552 Planarity : 0.004 0.039 2656 Dihedral : 11.625 174.818 3028 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.48 % Allowed : 15.00 % Favored : 84.52 % 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: 2.16 (0.20), residues: 1852 helix: 2.20 (0.15), residues: 1096 sheet: 0.77 (0.32), residues: 256 loop : 0.13 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 322 TYR 0.013 0.001 TYR C 497 PHE 0.013 0.001 PHE A 428 TRP 0.006 0.001 TRP B 345 HIS 0.005 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.12 (16180) covalent geometry : angle 0.49926 / 0.26 (21968) hydrogen bonds : bond 0.04892 / 3.25 ( 1032) hydrogen bonds : angle 4.65306 / 3.33 ( 3180) link_BETA1-4 : bond 0.00090 / 0.04 ( 4) link_BETA1-4 : angle 2.15834 / 1.08 ( 12) link_NAG-ASN : bond 0.00067 / 0.03 ( 4) link_NAG-ASN : angle 1.35898 / 0.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.415 Fit side-chains REVERT: A 322 ARG cc_start: 0.6206 (mmm-85) cc_final: 0.5755 (mtp85) REVERT: A 326 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6399 (mt) REVERT: B 285 LYS cc_start: 0.7692 (mtmm) cc_final: 0.7430 (mttm) REVERT: B 322 ARG cc_start: 0.6197 (mmm-85) cc_final: 0.5906 (mtp85) REVERT: C 285 LYS cc_start: 0.7684 (mtmm) cc_final: 0.7429 (mttm) REVERT: C 322 ARG cc_start: 0.6109 (mmm-85) cc_final: 0.5759 (mtp85) REVERT: C 326 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6447 (mt) REVERT: D 285 LYS cc_start: 0.7681 (mtmm) cc_final: 0.7425 (mttm) REVERT: D 322 ARG cc_start: 0.6197 (mmm-85) cc_final: 0.5918 (mtp85) outliers start: 8 outliers final: 0 residues processed: 127 average time/residue: 0.7030 time to fit residues: 96.5093 Evaluate side-chains 126 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain C residue 326 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 52 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 168 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 ASN B 234 HIS B 352 ASN C 352 ASN D 352 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107237 restraints weight = 14467.773| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.16 r_work: 0.3105 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16188 Z= 0.186 Angle : 0.601 6.031 21992 Z= 0.314 Chirality : 0.044 0.132 2552 Planarity : 0.004 0.038 2656 Dihedral : 11.636 174.004 3028 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.43 % Allowed : 13.75 % Favored : 84.82 % 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: 1.94 (0.20), residues: 1852 helix: 2.00 (0.15), residues: 1104 sheet: 0.83 (0.32), residues: 260 loop : -0.04 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 427 TYR 0.015 0.002 TYR D 497 PHE 0.018 0.002 PHE A 235 TRP 0.009 0.001 TRP B 491 HIS 0.006 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (16180) covalent geometry : angle 0.59528 / 0.31 (21968) hydrogen bonds : bond 0.06227 / 4.14 ( 1032) hydrogen bonds : angle 5.02859 / 3.60 ( 3180) link_BETA1-4 : bond 0.00359 / 0.18 ( 4) link_BETA1-4 : angle 2.69569 / 1.37 ( 12) link_NAG-ASN : bond 0.00344 / 0.17 ( 4) link_NAG-ASN : angle 2.63269 / 1.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6264 (mmm-85) cc_final: 0.5726 (mtp85) REVERT: A 326 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6478 (mt) REVERT: B 285 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7475 (mttp) REVERT: B 322 ARG cc_start: 0.6148 (mmm-85) cc_final: 0.5825 (mtp85) REVERT: B 326 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6394 (mt) REVERT: C 285 LYS cc_start: 0.7749 (mtmm) cc_final: 0.7477 (mttp) REVERT: C 322 ARG cc_start: 0.6281 (mmm-85) cc_final: 0.5684 (mtp85) REVERT: C 326 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6425 (mt) REVERT: D 285 LYS cc_start: 0.7745 (mtmm) cc_final: 0.7470 (mttp) REVERT: D 322 ARG cc_start: 0.6181 (mmm-85) cc_final: 0.5860 (mtp85) REVERT: D 326 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6418 (mt) outliers start: 24 outliers final: 19 residues processed: 146 average time/residue: 0.6473 time to fit residues: 102.7369 Evaluate side-chains 149 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 425 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 39 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 157 optimal weight: 0.1980 chunk 35 optimal weight: 0.1980 chunk 182 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.150292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111491 restraints weight = 14605.007| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.16 r_work: 0.3172 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16188 Z= 0.112 Angle : 0.492 6.059 21992 Z= 0.256 Chirality : 0.039 0.131 2552 Planarity : 0.004 0.039 2656 Dihedral : 11.265 174.081 3028 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.01 % Allowed : 14.76 % Favored : 84.23 % 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: 2.18 (0.20), residues: 1852 helix: 2.22 (0.15), residues: 1096 sheet: 0.79 (0.32), residues: 256 loop : 0.12 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 322 TYR 0.012 0.001 TYR B 497 PHE 0.013 0.001 PHE C 428 TRP 0.006 0.001 TRP D 345 HIS 0.005 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (16180) covalent geometry : angle 0.48913 / 0.26 (21968) hydrogen bonds : bond 0.04740 / 3.15 ( 1032) hydrogen bonds : angle 4.57944 / 3.28 ( 3180) link_BETA1-4 : bond 0.00084 / 0.04 ( 4) link_BETA1-4 : angle 2.13662 / 1.08 ( 12) link_NAG-ASN : bond 0.00012 / 0.01 ( 4) link_NAG-ASN : angle 1.23633 / 0.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6080 (mmm-85) cc_final: 0.5853 (mtp85) REVERT: B 285 LYS cc_start: 0.7677 (mtmm) cc_final: 0.7428 (mttm) REVERT: B 322 ARG cc_start: 0.6163 (mmm-85) cc_final: 0.5944 (mtp85) REVERT: C 285 LYS cc_start: 0.7681 (mtmm) cc_final: 0.7430 (mttm) REVERT: C 322 ARG cc_start: 0.6030 (mmm-85) cc_final: 0.5697 (mtp85) REVERT: C 326 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6453 (mt) REVERT: D 285 LYS cc_start: 0.7676 (mtmm) cc_final: 0.7421 (mttm) REVERT: D 322 ARG cc_start: 0.6163 (mmm-85) cc_final: 0.5934 (mtp85) outliers start: 17 outliers final: 8 residues processed: 143 average time/residue: 0.6529 time to fit residues: 101.7917 Evaluate side-chains 132 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 425 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 8.9990 chunk 16 optimal weight: 0.0670 chunk 5 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 overall best weight: 3.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS B 234 HIS C 234 HIS D 234 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107103 restraints weight = 14404.183| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.15 r_work: 0.3104 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16188 Z= 0.186 Angle : 0.598 5.766 21992 Z= 0.313 Chirality : 0.044 0.140 2552 Planarity : 0.004 0.038 2656 Dihedral : 11.340 173.939 3028 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.55 % Allowed : 15.18 % Favored : 83.27 % 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: 1.99 (0.20), residues: 1852 helix: 2.04 (0.15), residues: 1104 sheet: 0.85 (0.32), residues: 260 loop : 0.00 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 298 TYR 0.015 0.002 TYR B 497 PHE 0.018 0.002 PHE B 235 TRP 0.009 0.001 TRP B 491 HIS 0.005 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (16180) covalent geometry : angle 0.59213 / 0.31 (21968) hydrogen bonds : bond 0.06187 / 4.11 ( 1032) hydrogen bonds : angle 5.00435 / 3.59 ( 3180) link_BETA1-4 : bond 0.00302 / 0.15 ( 4) link_BETA1-4 : angle 2.72931 / 1.40 ( 12) link_NAG-ASN : bond 0.00327 / 0.16 ( 4) link_NAG-ASN : angle 2.62675 / 1.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6090 (mmm-85) cc_final: 0.5759 (mtp85) REVERT: A 326 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6482 (mt) REVERT: B 285 LYS cc_start: 0.7738 (mtmm) cc_final: 0.7470 (mttm) REVERT: B 322 ARG cc_start: 0.6211 (mmm-85) cc_final: 0.5901 (mtp85) REVERT: B 326 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6394 (mt) REVERT: C 285 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7477 (mttm) REVERT: C 322 ARG cc_start: 0.6184 (mmm-85) cc_final: 0.5646 (mtp85) REVERT: C 326 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6403 (mt) REVERT: D 285 LYS cc_start: 0.7745 (mtmm) cc_final: 0.7473 (mttm) REVERT: D 322 ARG cc_start: 0.6204 (mmm-85) cc_final: 0.5896 (mtp85) REVERT: D 326 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6418 (mt) outliers start: 26 outliers final: 15 residues processed: 153 average time/residue: 0.6442 time to fit residues: 107.5249 Evaluate side-chains 148 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 425 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS B 194 GLN B 234 HIS C 194 GLN C 234 HIS D 194 GLN D 234 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.148445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108958 restraints weight = 14536.926| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.16 r_work: 0.3133 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16188 Z= 0.137 Angle : 0.539 5.771 21992 Z= 0.281 Chirality : 0.041 0.134 2552 Planarity : 0.004 0.037 2656 Dihedral : 11.185 173.519 3028 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.65 % Allowed : 16.07 % Favored : 83.27 % 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: 2.09 (0.20), residues: 1852 helix: 2.15 (0.15), residues: 1096 sheet: 0.73 (0.32), residues: 256 loop : 0.09 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 336 TYR 0.014 0.002 TYR A 497 PHE 0.014 0.002 PHE A 428 TRP 0.007 0.001 TRP A 491 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (16180) covalent geometry : angle 0.53435 / 0.28 (21968) hydrogen bonds : bond 0.05392 / 3.58 ( 1032) hydrogen bonds : angle 4.78565 / 3.43 ( 3180) link_BETA1-4 : bond 0.00084 / 0.04 ( 4) link_BETA1-4 : angle 2.41043 / 1.21 ( 12) link_NAG-ASN : bond 0.00127 / 0.06 ( 4) link_NAG-ASN : angle 1.94734 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6082 (mmm-85) cc_final: 0.5762 (mtp85) REVERT: A 326 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6477 (mt) REVERT: B 285 LYS cc_start: 0.7688 (mtmm) cc_final: 0.7422 (mttm) REVERT: B 322 ARG cc_start: 0.6159 (mmm-85) cc_final: 0.5875 (mtp85) REVERT: B 326 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6397 (mt) REVERT: C 285 LYS cc_start: 0.7699 (mtmm) cc_final: 0.7432 (mttm) REVERT: C 322 ARG cc_start: 0.6085 (mmm-85) cc_final: 0.5715 (mtp85) REVERT: C 326 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6433 (mt) REVERT: D 285 LYS cc_start: 0.7694 (mtmm) cc_final: 0.7427 (mttm) REVERT: D 322 ARG cc_start: 0.6145 (mmm-85) cc_final: 0.5862 (mtp85) REVERT: D 326 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6405 (mt) outliers start: 11 outliers final: 5 residues processed: 136 average time/residue: 0.6433 time to fit residues: 95.4486 Evaluate side-chains 133 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 331 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 137 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107026 restraints weight = 14365.342| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.16 r_work: 0.3101 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16188 Z= 0.185 Angle : 0.608 5.858 21992 Z= 0.317 Chirality : 0.044 0.154 2552 Planarity : 0.004 0.038 2656 Dihedral : 11.260 173.442 3028 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.83 % Allowed : 16.01 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.20), residues: 1852 helix: 1.99 (0.15), residues: 1104 sheet: 0.82 (0.32), residues: 260 loop : -0.07 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 298 TYR 0.016 0.002 TYR A 404 PHE 0.018 0.002 PHE B 235 TRP 0.009 0.001 TRP B 491 HIS 0.005 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (16180) covalent geometry : angle 0.60170 / 0.32 (21968) hydrogen bonds : bond 0.06197 / 4.12 ( 1032) hydrogen bonds : angle 5.01516 / 3.60 ( 3180) link_BETA1-4 : bond 0.00351 / 0.18 ( 4) link_BETA1-4 : angle 2.73256 / 1.40 ( 12) link_NAG-ASN : bond 0.00307 / 0.15 ( 4) link_NAG-ASN : angle 2.53601 / 1.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6039 (mmm-85) cc_final: 0.5716 (mtp85) REVERT: A 326 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6505 (mt) REVERT: B 285 LYS cc_start: 0.7741 (mtmm) cc_final: 0.7478 (mttm) REVERT: B 322 ARG cc_start: 0.6181 (mmm-85) cc_final: 0.5816 (mtp85) REVERT: B 326 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6417 (mt) REVERT: C 285 LYS cc_start: 0.7745 (mtmm) cc_final: 0.7482 (mttm) REVERT: C 322 ARG cc_start: 0.6173 (mmm-85) cc_final: 0.5650 (mtp85) REVERT: C 326 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6490 (mt) REVERT: D 285 LYS cc_start: 0.7749 (mtmm) cc_final: 0.7484 (mttp) REVERT: D 322 ARG cc_start: 0.6166 (mmm-85) cc_final: 0.5805 (mtp85) REVERT: D 326 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6487 (mt) outliers start: 14 outliers final: 9 residues processed: 138 average time/residue: 0.6948 time to fit residues: 104.3590 Evaluate side-chains 136 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 88 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN B 69 GLN C 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.146870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107326 restraints weight = 14462.614| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.16 r_work: 0.3106 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16188 Z= 0.176 Angle : 0.595 5.800 21992 Z= 0.310 Chirality : 0.043 0.149 2552 Planarity : 0.004 0.039 2656 Dihedral : 11.239 173.236 3028 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.31 % Allowed : 15.24 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.20), residues: 1852 helix: 1.97 (0.15), residues: 1104 sheet: 0.89 (0.32), residues: 260 loop : -0.06 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 298 TYR 0.015 0.002 TYR A 497 PHE 0.017 0.002 PHE B 235 TRP 0.008 0.001 TRP C 491 HIS 0.005 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (16180) covalent geometry : angle 0.58943 / 0.31 (21968) hydrogen bonds : bond 0.06021 / 4.00 ( 1032) hydrogen bonds : angle 4.97835 / 3.57 ( 3180) link_BETA1-4 : bond 0.00315 / 0.16 ( 4) link_BETA1-4 : angle 2.67161 / 1.35 ( 12) link_NAG-ASN : bond 0.00256 / 0.13 ( 4) link_NAG-ASN : angle 2.32124 / 1.34 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6050 (mmm-85) cc_final: 0.5605 (mtp85) REVERT: A 326 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6473 (mt) REVERT: B 285 LYS cc_start: 0.7744 (mtmm) cc_final: 0.7479 (mttm) REVERT: B 322 ARG cc_start: 0.6126 (mmm-85) cc_final: 0.5758 (mtp85) REVERT: B 326 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6404 (mt) REVERT: C 285 LYS cc_start: 0.7749 (mtmm) cc_final: 0.7482 (mttm) REVERT: C 326 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6484 (mt) REVERT: D 285 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7484 (mttm) REVERT: D 322 ARG cc_start: 0.6111 (mmm-85) cc_final: 0.5744 (mtp85) REVERT: D 326 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6473 (mt) outliers start: 22 outliers final: 14 residues processed: 140 average time/residue: 0.6921 time to fit residues: 105.1927 Evaluate side-chains 139 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 425 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 130 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN C 69 GLN D 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107042 restraints weight = 14385.851| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.16 r_work: 0.3100 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16188 Z= 0.188 Angle : 0.619 6.134 21992 Z= 0.323 Chirality : 0.044 0.161 2552 Planarity : 0.004 0.039 2656 Dihedral : 11.266 173.823 3028 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.19 % Allowed : 15.54 % Favored : 83.27 % 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: 1.85 (0.20), residues: 1852 helix: 1.92 (0.15), residues: 1104 sheet: 0.86 (0.32), residues: 260 loop : -0.08 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 322 TYR 0.016 0.002 TYR C 404 PHE 0.018 0.002 PHE B 235 TRP 0.008 0.001 TRP B 491 HIS 0.005 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (16180) covalent geometry : angle 0.61301 / 0.32 (21968) hydrogen bonds : bond 0.06259 / 4.16 ( 1032) hydrogen bonds : angle 5.05201 / 3.62 ( 3180) link_BETA1-4 : bond 0.00389 / 0.19 ( 4) link_BETA1-4 : angle 2.76214 / 1.41 ( 12) link_NAG-ASN : bond 0.00307 / 0.15 ( 4) link_NAG-ASN : angle 2.54525 / 1.46 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5972.78 seconds wall clock time: 102 minutes 21.63 seconds (6141.63 seconds total)