Starting phenix.real_space_refine on Sat Sep 12 14:03:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sq9_25380/09_2026/7sq9_25380_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sq9_25380/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7sq9_25380/09_2026/7sq9_25380_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sq9_25380/09_2026/7sq9_25380_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sq9_25380/09_2026/7sq9_25380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sq9_25380/09_2026/7sq9_25380.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 122 Unusual residues: {' NA': 2, 'A4I': 1, 'EUJ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 3.94, per 1000 atoms: 0.25 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: 1.24 Conformation dependent library (CDL) restraints added in 726.8 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: 0.37 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: 2.51 Time building geometry restraints manager: 1.66 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: 1.700 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: 15.840 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- 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 : 0.608 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.8721 time to fit residues: 142.8607 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 : 0.595 ------------------------------------------------------------------------------- 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 469 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110493 restraints weight = 14609.920| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.15 r_work: 0.3155 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16188 Z= 0.134 Angle : 0.599 9.085 21992 Z= 0.293 Chirality : 0.042 0.182 2552 Planarity : 0.004 0.036 2656 Dihedral : 14.484 175.769 3028 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.19 % Allowed : 13.21 % Favored : 85.60 % 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: 2.12 (0.20), residues: 1852 helix: 2.09 (0.16), residues: 1116 sheet: 0.84 (0.32), residues: 260 loop : 0.16 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 151 TYR 0.013 0.001 TYR A 497 PHE 0.015 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 0.00257 / 0.13 (16180) covalent geometry : angle 0.59545 / 0.29 (21968) hydrogen bonds : bond 0.05185 / 3.44 ( 1032) hydrogen bonds : angle 4.92016 / 3.52 ( 3180) link_BETA1-4 : bond 0.00358 / 0.19 ( 4) link_BETA1-4 : angle 2.22857 / 1.17 ( 12) link_NAG-ASN : bond 0.00245 / 0.12 ( 4) link_NAG-ASN : angle 1.69879 / 1.00 ( 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 157 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.619 Fit side-chains REVERT: A 247 ASN cc_start: 0.8471 (t0) cc_final: 0.8171 (m110) REVERT: A 322 ARG cc_start: 0.6238 (mmm-85) cc_final: 0.5576 (ttm-80) REVERT: B 247 ASN cc_start: 0.8445 (t0) cc_final: 0.8150 (m110) REVERT: B 322 ARG cc_start: 0.6276 (mmm-85) cc_final: 0.5427 (ttm-80) REVERT: C 247 ASN cc_start: 0.8414 (t0) cc_final: 0.8126 (m110) REVERT: C 322 ARG cc_start: 0.6275 (mmm-85) cc_final: 0.5443 (ttm-80) REVERT: D 247 ASN cc_start: 0.8440 (t0) cc_final: 0.8154 (m110) REVERT: D 322 ARG cc_start: 0.6291 (mmm-85) cc_final: 0.5429 (ttm-80) outliers start: 20 outliers final: 4 residues processed: 145 average time/residue: 0.7418 time to fit residues: 117.3641 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 : 0.535 ------------------------------------------------------------------------------- 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: 9.9990 chunk 27 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS A 327 GLN A 352 ASN B 234 HIS B 327 GLN B 352 ASN C 234 HIS C 352 ASN D 234 HIS D 327 GLN D 352 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106603 restraints weight = 14564.646| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.15 r_work: 0.3095 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.0995 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= 0.203 Angle : 0.640 6.522 21992 Z= 0.331 Chirality : 0.045 0.138 2552 Planarity : 0.005 0.037 2656 Dihedral : 12.189 174.510 3028 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.61 % Allowed : 12.98 % Favored : 85.42 % 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: 1.88 (0.20), residues: 1852 helix: 1.94 (0.15), residues: 1104 sheet: 0.83 (0.32), residues: 260 loop : -0.03 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 151 TYR 0.015 0.002 TYR C 404 PHE 0.018 0.003 PHE B 235 TRP 0.009 0.001 TRP B 491 HIS 0.006 0.002 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (16180) covalent geometry : angle 0.63301 / 0.33 (21968) hydrogen bonds : bond 0.06563 / 4.36 ( 1032) hydrogen bonds : angle 5.17761 / 3.70 ( 3180) link_BETA1-4 : bond 0.00405 / 0.20 ( 4) link_BETA1-4 : angle 2.78437 / 1.42 ( 12) link_NAG-ASN : bond 0.00464 / 0.23 ( 4) link_NAG-ASN : angle 2.91169 / 1.67 ( 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 155 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.623 Fit side-chains REVERT: A 322 ARG cc_start: 0.6283 (mmm-85) cc_final: 0.5543 (ttm-80) REVERT: A 326 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6468 (mt) REVERT: B 322 ARG cc_start: 0.6223 (mmm-85) cc_final: 0.5449 (ttm-80) REVERT: B 326 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6464 (mt) REVERT: C 322 ARG cc_start: 0.6235 (mmm-85) cc_final: 0.5472 (ttm-80) REVERT: C 326 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6483 (mt) REVERT: D 322 ARG cc_start: 0.6226 (mmm-85) cc_final: 0.5450 (ttm-80) REVERT: D 326 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6463 (mt) outliers start: 27 outliers final: 23 residues processed: 148 average time/residue: 0.7345 time to fit residues: 118.8405 Evaluate side-chains 147 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 249 GLU 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 249 GLU 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: 9.9990 chunk 166 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.147202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107617 restraints weight = 14505.010| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.16 r_work: 0.3110 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16188 Z= 0.163 Angle : 0.576 6.199 21992 Z= 0.301 Chirality : 0.042 0.132 2552 Planarity : 0.004 0.037 2656 Dihedral : 11.945 173.798 3028 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.19 % Allowed : 14.17 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.20), residues: 1852 helix: 1.99 (0.15), residues: 1104 sheet: 0.78 (0.33), residues: 256 loop : 0.00 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 151 TYR 0.014 0.002 TYR D 497 PHE 0.016 0.002 PHE D 235 TRP 0.008 0.001 TRP A 491 HIS 0.006 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (16180) covalent geometry : angle 0.57055 / 0.30 (21968) hydrogen bonds : bond 0.05912 / 3.93 ( 1032) hydrogen bonds : angle 4.98153 / 3.56 ( 3180) link_BETA1-4 : bond 0.00256 / 0.13 ( 4) link_BETA1-4 : angle 2.59918 / 1.31 ( 12) link_NAG-ASN : bond 0.00214 / 0.11 ( 4) link_NAG-ASN : angle 2.29778 / 1.32 ( 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 144 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.551 Fit side-chains REVERT: A 322 ARG cc_start: 0.6249 (mmm-85) cc_final: 0.5638 (mtp85) REVERT: A 326 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6403 (mt) REVERT: B 285 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7467 (mttm) REVERT: B 322 ARG cc_start: 0.6239 (mmm-85) cc_final: 0.5492 (ttm-80) REVERT: B 326 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6408 (mt) REVERT: C 285 LYS cc_start: 0.7739 (mtmm) cc_final: 0.7471 (mttm) REVERT: C 322 ARG cc_start: 0.6250 (mmm-85) cc_final: 0.5507 (ttm-80) REVERT: C 326 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6408 (mt) REVERT: D 285 LYS cc_start: 0.7736 (mtmm) cc_final: 0.7471 (mttm) REVERT: D 322 ARG cc_start: 0.6241 (mmm-85) cc_final: 0.5493 (ttm-80) REVERT: D 326 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6408 (mt) outliers start: 20 outliers final: 12 residues processed: 140 average time/residue: 0.7935 time to fit residues: 120.5953 Evaluate side-chains 139 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 217 SER Chi-restraints excluded: chain A residue 326 LEU 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 52 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.146946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107297 restraints weight = 14558.905| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.16 r_work: 0.3107 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16188 Z= 0.168 Angle : 0.580 5.925 21992 Z= 0.304 Chirality : 0.043 0.133 2552 Planarity : 0.004 0.037 2656 Dihedral : 11.745 173.336 3028 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.96 % Allowed : 13.04 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.20), residues: 1852 helix: 1.94 (0.15), residues: 1104 sheet: 0.89 (0.32), residues: 260 loop : -0.05 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 151 TYR 0.015 0.002 TYR B 497 PHE 0.016 0.002 PHE D 235 TRP 0.009 0.001 TRP A 491 HIS 0.006 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (16180) covalent geometry : angle 0.57432 / 0.30 (21968) hydrogen bonds : bond 0.06023 / 4.01 ( 1032) hydrogen bonds : angle 4.98546 / 3.57 ( 3180) link_BETA1-4 : bond 0.00279 / 0.14 ( 4) link_BETA1-4 : angle 2.61115 / 1.33 ( 12) link_NAG-ASN : bond 0.00260 / 0.13 ( 4) link_NAG-ASN : angle 2.46154 / 1.41 ( 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 165 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6185 (mmm-85) cc_final: 0.5646 (mtp85) REVERT: A 326 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6479 (mt) REVERT: B 285 LYS cc_start: 0.7733 (mtmm) cc_final: 0.7478 (mttm) REVERT: B 322 ARG cc_start: 0.6225 (mmm-85) cc_final: 0.5613 (mtp85) REVERT: B 326 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6422 (mt) REVERT: C 285 LYS cc_start: 0.7700 (mtmm) cc_final: 0.7434 (mttm) REVERT: C 322 ARG cc_start: 0.6229 (mmm-85) cc_final: 0.5621 (mtp85) REVERT: C 326 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6423 (mt) REVERT: D 285 LYS cc_start: 0.7699 (mtmm) cc_final: 0.7440 (mttm) REVERT: D 322 ARG cc_start: 0.6222 (mmm-85) cc_final: 0.5611 (mtp85) REVERT: D 326 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6425 (mt) outliers start: 33 outliers final: 25 residues processed: 156 average time/residue: 0.7405 time to fit residues: 126.1830 Evaluate side-chains 152 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 217 SER Chi-restraints excluded: chain A residue 249 GLU 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 217 SER 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 217 SER 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 217 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 39 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 182 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.147877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108647 restraints weight = 14565.094| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.16 r_work: 0.3126 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16188 Z= 0.141 Angle : 0.542 5.863 21992 Z= 0.283 Chirality : 0.041 0.130 2552 Planarity : 0.004 0.038 2656 Dihedral : 11.526 173.394 3028 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.55 % Allowed : 14.05 % Favored : 84.40 % 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 (0.20), residues: 1852 helix: 2.08 (0.15), residues: 1104 sheet: 0.83 (0.32), residues: 256 loop : 0.03 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 336 TYR 0.014 0.002 TYR A 497 PHE 0.015 0.002 PHE A 428 TRP 0.008 0.001 TRP C 491 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (16180) covalent geometry : angle 0.53686 / 0.28 (21968) hydrogen bonds : bond 0.05513 / 3.67 ( 1032) hydrogen bonds : angle 4.82934 / 3.46 ( 3180) link_BETA1-4 : bond 0.00124 / 0.06 ( 4) link_BETA1-4 : angle 2.42720 / 1.22 ( 12) link_NAG-ASN : bond 0.00154 / 0.08 ( 4) link_NAG-ASN : angle 2.01105 / 1.16 ( 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 149 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6166 (mmm-85) cc_final: 0.5867 (mtp85) REVERT: B 285 LYS cc_start: 0.7700 (mtmm) cc_final: 0.7442 (mttm) REVERT: B 322 ARG cc_start: 0.6175 (mmm-85) cc_final: 0.5743 (mtp85) REVERT: B 326 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6407 (mt) REVERT: C 285 LYS cc_start: 0.7706 (mtmm) cc_final: 0.7439 (mttm) REVERT: C 322 ARG cc_start: 0.6179 (mmm-85) cc_final: 0.5752 (mtp85) REVERT: C 326 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6396 (mt) REVERT: D 285 LYS cc_start: 0.7703 (mtmm) cc_final: 0.7445 (mttm) REVERT: D 322 ARG cc_start: 0.6165 (mmm-85) cc_final: 0.5738 (mtp85) REVERT: D 326 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6411 (mt) outliers start: 26 outliers final: 22 residues processed: 144 average time/residue: 0.7603 time to fit residues: 119.1073 Evaluate side-chains 148 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 217 SER 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 217 SER Chi-restraints excluded: chain B residue 249 GLU 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 B residue 472 ASP Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 217 SER 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 C residue 472 ASP Chi-restraints excluded: chain D residue 67 MET 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 Chi-restraints excluded: chain D residue 472 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 78 optimal weight: 0.2980 chunk 3 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 overall best weight: 2.6584 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.146938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107340 restraints weight = 14453.494| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.16 r_work: 0.3109 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16188 Z= 0.168 Angle : 0.580 5.782 21992 Z= 0.304 Chirality : 0.043 0.139 2552 Planarity : 0.004 0.038 2656 Dihedral : 11.517 173.232 3028 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.90 % Allowed : 14.23 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.20), residues: 1852 helix: 1.97 (0.15), residues: 1104 sheet: 0.87 (0.32), residues: 260 loop : -0.07 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 336 TYR 0.015 0.002 TYR A 497 PHE 0.017 0.002 PHE B 235 TRP 0.009 0.001 TRP A 491 HIS 0.006 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (16180) covalent geometry : angle 0.57424 / 0.30 (21968) hydrogen bonds : bond 0.06023 / 4.01 ( 1032) hydrogen bonds : angle 4.96806 / 3.56 ( 3180) link_BETA1-4 : bond 0.00264 / 0.13 ( 4) link_BETA1-4 : angle 2.61602 / 1.33 ( 12) link_NAG-ASN : bond 0.00274 / 0.14 ( 4) link_NAG-ASN : angle 2.47955 / 1.42 ( 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 163 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6087 (mmm-85) cc_final: 0.5745 (mtp85) REVERT: A 326 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6470 (mt) REVERT: B 285 LYS cc_start: 0.7712 (mtmm) cc_final: 0.7448 (mttm) REVERT: B 322 ARG cc_start: 0.6176 (mmm-85) cc_final: 0.5639 (mtp85) REVERT: B 326 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6416 (mt) REVERT: C 285 LYS cc_start: 0.7703 (mtmm) cc_final: 0.7442 (mttm) REVERT: C 322 ARG cc_start: 0.6203 (mmm-85) cc_final: 0.5657 (mtp85) REVERT: C 326 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6400 (mt) REVERT: D 285 LYS cc_start: 0.7703 (mtmm) cc_final: 0.7436 (mttm) REVERT: D 322 ARG cc_start: 0.6173 (mmm-85) cc_final: 0.5637 (mtp85) REVERT: D 326 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6422 (mt) outliers start: 32 outliers final: 24 residues processed: 159 average time/residue: 0.7672 time to fit residues: 132.9319 Evaluate side-chains 153 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 217 SER 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 217 SER 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 217 SER 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 217 SER 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: 9.9990 chunk 42 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.147161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107826 restraints weight = 14599.806| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.16 r_work: 0.3115 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16188 Z= 0.158 Angle : 0.565 5.867 21992 Z= 0.296 Chirality : 0.042 0.139 2552 Planarity : 0.004 0.038 2656 Dihedral : 11.480 173.333 3028 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.49 % Allowed : 14.58 % Favored : 83.93 % 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: 2.02 (0.15), residues: 1104 sheet: 0.76 (0.32), residues: 256 loop : 0.01 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.014 0.002 TYR B 497 PHE 0.015 0.002 PHE D 235 TRP 0.009 0.001 TRP C 491 HIS 0.004 0.001 HIS C 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (16180) covalent geometry : angle 0.55948 / 0.29 (21968) hydrogen bonds : bond 0.05802 / 3.86 ( 1032) hydrogen bonds : angle 4.91014 / 3.52 ( 3180) link_BETA1-4 : bond 0.00191 / 0.10 ( 4) link_BETA1-4 : angle 2.57050 / 1.30 ( 12) link_NAG-ASN : bond 0.00199 / 0.10 ( 4) link_NAG-ASN : angle 2.26487 / 1.30 ( 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 153 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6044 (mmm-85) cc_final: 0.5712 (mtp85) REVERT: A 326 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6462 (mt) REVERT: B 285 LYS cc_start: 0.7704 (mtmm) cc_final: 0.7440 (mttm) REVERT: B 322 ARG cc_start: 0.6154 (mmm-85) cc_final: 0.5644 (mtp85) REVERT: B 326 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6395 (mt) REVERT: C 285 LYS cc_start: 0.7702 (mtmm) cc_final: 0.7433 (mttm) REVERT: C 322 ARG cc_start: 0.6158 (mmm-85) cc_final: 0.5658 (mtp85) REVERT: C 326 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6391 (mt) REVERT: D 285 LYS cc_start: 0.7708 (mtmm) cc_final: 0.7441 (mttm) REVERT: D 322 ARG cc_start: 0.6213 (mmm-85) cc_final: 0.5689 (mtp85) REVERT: D 326 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6411 (mt) outliers start: 25 outliers final: 21 residues processed: 149 average time/residue: 0.7835 time to fit residues: 126.9813 Evaluate side-chains 150 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 A residue 472 ASP Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 92 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 137 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.147766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108358 restraints weight = 14502.364| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.17 r_work: 0.3124 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16188 Z= 0.144 Angle : 0.544 5.917 21992 Z= 0.285 Chirality : 0.041 0.145 2552 Planarity : 0.004 0.038 2656 Dihedral : 11.344 173.684 3028 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.61 % Allowed : 14.11 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.20), residues: 1852 helix: 2.08 (0.15), residues: 1104 sheet: 0.78 (0.32), residues: 256 loop : 0.01 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 336 TYR 0.014 0.002 TYR B 497 PHE 0.015 0.002 PHE D 428 TRP 0.008 0.001 TRP A 491 HIS 0.006 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (16180) covalent geometry : angle 0.53888 / 0.28 (21968) hydrogen bonds : bond 0.05571 / 3.70 ( 1032) hydrogen bonds : angle 4.83452 / 3.46 ( 3180) link_BETA1-4 : bond 0.00168 / 0.08 ( 4) link_BETA1-4 : angle 2.46553 / 1.25 ( 12) link_NAG-ASN : bond 0.00149 / 0.07 ( 4) link_NAG-ASN : angle 2.05412 / 1.18 ( 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 152 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6007 (mmm-85) cc_final: 0.5690 (mtp85) REVERT: A 326 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6473 (mt) REVERT: B 285 LYS cc_start: 0.7698 (mtmm) cc_final: 0.7440 (mttm) REVERT: B 322 ARG cc_start: 0.6167 (mmm-85) cc_final: 0.5798 (mtp85) REVERT: B 326 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6407 (mt) REVERT: C 285 LYS cc_start: 0.7701 (mtmm) cc_final: 0.7438 (mttm) REVERT: C 322 ARG cc_start: 0.6175 (mmm-85) cc_final: 0.5871 (mtp85) REVERT: D 285 LYS cc_start: 0.7701 (mtmm) cc_final: 0.7441 (mttm) REVERT: D 322 ARG cc_start: 0.6146 (mmm-85) cc_final: 0.5782 (mtp85) REVERT: D 326 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6429 (mt) outliers start: 27 outliers final: 21 residues processed: 148 average time/residue: 0.7572 time to fit residues: 122.2349 Evaluate side-chains 148 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 A residue 472 ASP Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 92 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 88 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107930 restraints weight = 14566.214| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.16 r_work: 0.3117 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16188 Z= 0.153 Angle : 0.559 5.976 21992 Z= 0.293 Chirality : 0.042 0.145 2552 Planarity : 0.004 0.038 2656 Dihedral : 11.324 174.004 3028 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.55 % Allowed : 14.29 % Favored : 84.17 % 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: 1.98 (0.20), residues: 1852 helix: 2.03 (0.15), residues: 1104 sheet: 0.81 (0.32), residues: 256 loop : 0.02 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.015 0.002 TYR B 497 PHE 0.016 0.002 PHE D 235 TRP 0.009 0.001 TRP A 491 HIS 0.006 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (16180) covalent geometry : angle 0.55334 / 0.29 (21968) hydrogen bonds : bond 0.05751 / 3.82 ( 1032) hydrogen bonds : angle 4.88864 / 3.50 ( 3180) link_BETA1-4 : bond 0.00190 / 0.10 ( 4) link_BETA1-4 : angle 2.52258 / 1.28 ( 12) link_NAG-ASN : bond 0.00195 / 0.10 ( 4) link_NAG-ASN : angle 2.28468 / 1.31 ( 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 154 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 ARG cc_start: 0.6017 (mmm-85) cc_final: 0.5704 (mtp85) REVERT: A 326 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6503 (mt) REVERT: B 285 LYS cc_start: 0.7701 (mtmm) cc_final: 0.7422 (mttm) REVERT: B 322 ARG cc_start: 0.6164 (mmm-85) cc_final: 0.5799 (mtp85) REVERT: B 326 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6432 (mt) REVERT: C 285 LYS cc_start: 0.7696 (mtmm) cc_final: 0.7424 (mttm) REVERT: C 322 ARG cc_start: 0.6169 (mmm-85) cc_final: 0.5804 (mtp85) REVERT: C 326 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6503 (mt) REVERT: D 285 LYS cc_start: 0.7703 (mtmm) cc_final: 0.7424 (mttm) REVERT: D 322 ARG cc_start: 0.6170 (mmm-85) cc_final: 0.5804 (mtp85) REVERT: D 326 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6524 (mt) outliers start: 26 outliers final: 22 residues processed: 150 average time/residue: 0.7591 time to fit residues: 124.2693 Evaluate side-chains 153 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 A residue 472 ASP Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 92 THR 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 C residue 472 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 130 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN A 292 HIS B 292 HIS C 292 HIS D 292 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107279 restraints weight = 14437.381| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.18 r_work: 0.3105 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16188 Z= 0.172 Angle : 0.586 5.837 21992 Z= 0.307 Chirality : 0.043 0.148 2552 Planarity : 0.004 0.038 2656 Dihedral : 11.375 173.891 3028 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.67 % Allowed : 14.40 % Favored : 83.93 % 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: 1.89 (0.20), residues: 1852 helix: 1.95 (0.15), residues: 1104 sheet: 0.86 (0.32), residues: 260 loop : -0.07 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.015 0.002 TYR D 404 PHE 0.017 0.002 PHE B 235 TRP 0.008 0.001 TRP D 491 HIS 0.007 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (16180) covalent geometry : angle 0.58013 / 0.31 (21968) hydrogen bonds : bond 0.06085 / 4.05 ( 1032) hydrogen bonds : angle 4.98501 / 3.57 ( 3180) link_BETA1-4 : bond 0.00283 / 0.14 ( 4) link_BETA1-4 : angle 2.64268 / 1.35 ( 12) link_NAG-ASN : bond 0.00260 / 0.13 ( 4) link_NAG-ASN : angle 2.50535 / 1.43 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7123.13 seconds wall clock time: 122 minutes 2.18 seconds (7322.18 seconds total)