Starting phenix.real_space_refine on Fri Jul 3 17:56:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sq6_25377/07_2026/7sq6_25377_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sq6_25377/07_2026/7sq6_25377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sq6_25377/07_2026/7sq6_25377_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sq6_25377/07_2026/7sq6_25377_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sq6_25377/07_2026/7sq6_25377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sq6_25377/07_2026/7sq6_25377.map" } resolution = 2.32 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 96 5.16 5 Na 2 4.78 5 C 10064 2.51 5 N 2532 2.21 5 O 2648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15342 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3777 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 14, 'TRANS': 452} Chain breaks: 2 Chain: "B" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3777 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 14, 'TRANS': 452} Chain breaks: 2 Chain: "C" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3777 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 14, 'TRANS': 452} Chain breaks: 2 Chain: "D" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3777 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 14, 'TRANS': 452} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.31, per 1000 atoms: 0.22 Number of scatterers: 15342 At special positions: 0 Unit cell: (108.73, 108.73, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 Na 2 11.00 O 2648 8.00 N 2532 7.00 C 10064 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: 1.13 Conformation dependent library (CDL) restraints added in 446.7 milliseconds 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 67.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.707A pdb=" N LYS A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.586A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 143 Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 216 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 297 through 338 Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 352 through 377 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.785A 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 412 through 448 Proline residue: A 423 - end of helix removed outlier: 3.627A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 4.119A 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: 3.823A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.903A 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: 3.707A pdb=" N LYS B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 60 Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.585A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 143 Proline residue: B 140 - end of helix Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 216 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 297 through 338 Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 352 through 377 Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.785A 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 412 through 448 Proline residue: B 423 - end of helix removed outlier: 3.627A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 4.118A 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: 3.823A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.903A 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: 3.706A pdb=" N LYS C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 60 Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.585A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 143 Proline residue: C 140 - end of helix Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 216 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 297 through 338 Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 352 through 377 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.785A 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 412 through 448 Proline residue: C 423 - end of helix removed outlier: 3.627A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 434 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 removed outlier: 4.118A 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: 3.823A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) removed outlier: 3.903A 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: 3.707A pdb=" N LYS D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 60 Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.586A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 143 Proline residue: D 140 - end of helix Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'D' and resid 216 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 297 through 338 Processing helix chain 'D' and resid 344 through 350 Processing helix chain 'D' and resid 352 through 377 Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.785A 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 412 through 448 Proline residue: D 423 - end of helix removed outlier: 3.626A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 434 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 removed outlier: 4.118A 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: 3.823A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) removed outlier: 3.903A 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: 6.715A pdb=" N ARG A 168 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 231 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS A 166 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A 233 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA A 164 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ARG A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLY A 173 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 7.439A 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: 6.716A pdb=" N ARG B 168 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 231 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS B 166 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE B 233 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA B 164 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ARG B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLY B 173 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 7.439A 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: 6.716A pdb=" N ARG C 168 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL C 231 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS C 166 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE C 233 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA C 164 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ARG C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLY C 173 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 7.439A 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: 6.715A pdb=" N ARG D 168 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL D 231 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS D 166 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE D 233 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA D 164 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ARG D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLY D 173 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASP D 185 " --> pdb=" O GLY D 173 " (cutoff:3.500A) 1144 hydrogen bonds defined for protein. 3216 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: 2.01 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2280 1.31 - 1.44: 4596 1.44 - 1.57: 8700 1.57 - 1.70: 4 1.70 - 1.83: 132 Bond restraints: 15712 Sorted by residual: bond pdb=" C15 AQV A 601 " pdb=" N2 AQV A 601 " ideal model delta sigma weight residual 1.423 1.543 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C15 AQV D 601 " pdb=" N2 AQV D 601 " ideal model delta sigma weight residual 1.423 1.543 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C15 AQV C 601 " pdb=" N2 AQV C 601 " ideal model delta sigma weight residual 1.423 1.543 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C15 AQV B 601 " pdb=" N2 AQV B 601 " ideal model delta sigma weight residual 1.423 1.543 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C10 AQV D 601 " pdb=" N2 AQV D 601 " ideal model delta sigma weight residual 1.367 1.482 -0.115 2.00e-02 2.50e+03 3.29e+01 ... (remaining 15707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 20612 2.14 - 4.28: 630 4.28 - 6.42: 66 6.42 - 8.56: 20 8.56 - 10.70: 4 Bond angle restraints: 21332 Sorted by residual: angle pdb=" CA LEU B 348 " pdb=" C LEU B 348 " pdb=" O LEU B 348 " ideal model delta sigma weight residual 121.00 116.82 4.18 1.05e+00 9.07e-01 1.59e+01 angle pdb=" CA LEU A 348 " pdb=" C LEU A 348 " pdb=" O LEU A 348 " ideal model delta sigma weight residual 121.00 116.84 4.16 1.05e+00 9.07e-01 1.57e+01 angle pdb=" CA LEU D 348 " pdb=" C LEU D 348 " pdb=" O LEU D 348 " ideal model delta sigma weight residual 121.00 116.84 4.16 1.05e+00 9.07e-01 1.57e+01 angle pdb=" CA LEU C 348 " pdb=" C LEU C 348 " pdb=" O LEU C 348 " ideal model delta sigma weight residual 121.00 116.84 4.16 1.05e+00 9.07e-01 1.57e+01 angle pdb=" N ARG A 347 " pdb=" CA ARG A 347 " pdb=" C ARG A 347 " ideal model delta sigma weight residual 111.11 106.45 4.66 1.20e+00 6.94e-01 1.51e+01 ... (remaining 21327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8160 17.97 - 35.94: 908 35.94 - 53.92: 176 53.92 - 71.89: 48 71.89 - 89.86: 32 Dihedral angle restraints: 9324 sinusoidal: 3840 harmonic: 5484 Sorted by residual: dihedral pdb=" C VAL C 332 " pdb=" N VAL C 332 " pdb=" CA VAL C 332 " pdb=" CB VAL C 332 " ideal model delta harmonic sigma weight residual -122.00 -131.14 9.14 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" C VAL B 332 " pdb=" N VAL B 332 " pdb=" CA VAL B 332 " pdb=" CB VAL B 332 " ideal model delta harmonic sigma weight residual -122.00 -131.14 9.14 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" C VAL A 332 " pdb=" N VAL A 332 " pdb=" CA VAL A 332 " pdb=" CB VAL A 332 " ideal model delta harmonic sigma weight residual -122.00 -131.14 9.14 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 9321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2059 0.067 - 0.133: 305 0.133 - 0.200: 49 0.200 - 0.267: 37 0.267 - 0.334: 10 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA ARG B 338 " pdb=" N ARG B 338 " pdb=" C ARG B 338 " pdb=" CB ARG B 338 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ARG C 338 " pdb=" N ARG C 338 " pdb=" C ARG C 338 " pdb=" CB ARG C 338 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ARG D 338 " pdb=" N ARG D 338 " pdb=" C ARG D 338 " pdb=" CB ARG D 338 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 2457 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 57 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C ARG D 57 " 0.051 2.00e-02 2.50e+03 pdb=" O ARG D 57 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA D 58 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 57 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C ARG A 57 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG A 57 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 58 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 57 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C ARG C 57 " 0.051 2.00e-02 2.50e+03 pdb=" O ARG C 57 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 58 " -0.017 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 6274 2.91 - 3.40: 15447 3.40 - 3.90: 26807 3.90 - 4.40: 30913 4.40 - 4.90: 49847 Nonbonded interactions: 129288 Sorted by model distance: nonbonded pdb=" OH TYR A 109 " pdb=" OD1 ASP A 114 " model vdw 2.408 3.040 nonbonded pdb=" OH TYR B 109 " pdb=" OD1 ASP B 114 " model vdw 2.408 3.040 nonbonded pdb=" OH TYR D 109 " pdb=" OD1 ASP D 114 " model vdw 2.408 3.040 nonbonded pdb=" OH TYR C 109 " pdb=" OD1 ASP C 114 " model vdw 2.408 3.040 nonbonded pdb=" O TYR A 47 " pdb=" NZ LYS A 55 " model vdw 2.436 3.120 ... (remaining 129283 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.730 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 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 : 0.007 0.120 15720 Z= 0.414 Angle : 0.817 10.700 21356 Z= 0.509 Chirality : 0.060 0.334 2460 Planarity : 0.005 0.044 2600 Dihedral : 16.321 89.861 5788 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 17.94 % Favored : 82.06 % 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: 1.57 (0.19), residues: 1844 helix: 1.57 (0.15), residues: 1116 sheet: 0.95 (0.31), residues: 252 loop : -0.02 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 403 TYR 0.014 0.002 TYR D 497 PHE 0.021 0.002 PHE A 474 TRP 0.009 0.002 TRP A 491 HIS 0.007 0.002 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.41 (15712) covalent geometry : angle 0.81228 / 0.51 (21332) hydrogen bonds : bond 0.12539 / 8.20 ( 1052) hydrogen bonds : angle 6.59061 / 4.70 ( 3216) link_BETA1-4 : bond 0.00564 / 0.28 ( 4) link_BETA1-4 : angle 2.20311 / 1.23 ( 12) link_NAG-ASN : bond 0.00062 / 0.03 ( 4) link_NAG-ASN : angle 3.07730 / 1.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.564 Fit side-chains REVERT: C 303 VAL cc_start: 0.7753 (t) cc_final: 0.7550 (p) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.4540 time to fit residues: 98.3993 Evaluate side-chains 153 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS A 469 ASN B 234 HIS B 469 ASN C 234 HIS C 469 ASN D 234 HIS D 469 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.137987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.095456 restraints weight = 15506.261| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.78 r_work: 0.2811 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15720 Z= 0.164 Angle : 0.556 6.334 21356 Z= 0.295 Chirality : 0.041 0.136 2460 Planarity : 0.004 0.038 2600 Dihedral : 6.648 53.708 2316 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.59 % Allowed : 14.83 % Favored : 81.58 % 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: 2.00 (0.19), residues: 1844 helix: 1.92 (0.15), residues: 1108 sheet: 1.10 (0.32), residues: 252 loop : 0.18 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 318 TYR 0.014 0.002 TYR A 497 PHE 0.019 0.002 PHE B 235 TRP 0.012 0.001 TRP C 157 HIS 0.005 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (15712) covalent geometry : angle 0.55189 / 0.29 (21332) hydrogen bonds : bond 0.05856 / 3.86 ( 1052) hydrogen bonds : angle 5.15572 / 3.68 ( 3216) link_BETA1-4 : bond 0.00020 / 0.01 ( 4) link_BETA1-4 : angle 1.80163 / 0.91 ( 12) link_NAG-ASN : bond 0.00067 / 0.03 ( 4) link_NAG-ASN : angle 2.25998 / 1.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 148 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 65 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7143 (mtmp) REVERT: A 95 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: A 358 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7965 (mp) REVERT: B 65 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7127 (mtmp) REVERT: B 95 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: B 358 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7965 (mp) REVERT: C 65 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7126 (mtmp) REVERT: C 358 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7973 (mp) REVERT: D 65 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7125 (mtmp) REVERT: D 95 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: D 358 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7965 (mp) outliers start: 60 outliers final: 17 residues processed: 187 average time/residue: 0.5743 time to fit residues: 118.2612 Evaluate side-chains 180 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 145 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 59 optimal weight: 0.1980 chunk 92 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.092272 restraints weight = 15730.610| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.51 r_work: 0.2868 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15720 Z= 0.139 Angle : 0.517 5.992 21356 Z= 0.272 Chirality : 0.040 0.125 2460 Planarity : 0.004 0.037 2600 Dihedral : 6.490 53.341 2316 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.57 % Allowed : 15.13 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.20), residues: 1844 helix: 2.12 (0.15), residues: 1108 sheet: 1.20 (0.31), residues: 252 loop : 0.34 (0.32), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 44 TYR 0.013 0.001 TYR C 497 PHE 0.015 0.002 PHE C 235 TRP 0.007 0.001 TRP C 157 HIS 0.004 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (15712) covalent geometry : angle 0.51350 / 0.27 (21332) hydrogen bonds : bond 0.05316 / 3.50 ( 1052) hydrogen bonds : angle 4.91455 / 3.51 ( 3216) link_BETA1-4 : bond 0.00043 / 0.02 ( 4) link_BETA1-4 : angle 1.79489 / 0.94 ( 12) link_NAG-ASN : bond 0.00059 / 0.03 ( 4) link_NAG-ASN : angle 1.82760 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.674 Fit side-chains REVERT: A 44 ARG cc_start: 0.5891 (OUTLIER) cc_final: 0.5451 (mtm-85) REVERT: A 65 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6898 (ttmt) REVERT: A 95 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: A 355 TYR cc_start: 0.8354 (m-10) cc_final: 0.7987 (m-10) REVERT: A 358 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7892 (mp) REVERT: B 44 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.5461 (mtm-85) REVERT: B 65 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6961 (ttmt) REVERT: B 95 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7895 (mp0) REVERT: B 358 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7920 (mp) REVERT: C 44 ARG cc_start: 0.5916 (OUTLIER) cc_final: 0.5552 (mtm-85) REVERT: C 65 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6953 (ttmt) REVERT: C 95 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: C 358 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7917 (mp) REVERT: D 44 ARG cc_start: 0.5919 (OUTLIER) cc_final: 0.5487 (mtm-85) REVERT: D 65 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6912 (ttmt) REVERT: D 95 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: D 355 TYR cc_start: 0.8362 (m-10) cc_final: 0.7994 (m-10) REVERT: D 358 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7907 (mp) outliers start: 43 outliers final: 9 residues processed: 177 average time/residue: 0.5319 time to fit residues: 104.4534 Evaluate side-chains 177 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 49 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.090524 restraints weight = 15626.271| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.45 r_work: 0.2830 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15720 Z= 0.202 Angle : 0.590 6.108 21356 Z= 0.312 Chirality : 0.043 0.132 2460 Planarity : 0.005 0.046 2600 Dihedral : 6.669 54.359 2316 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.77 % Allowed : 13.88 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.19), residues: 1844 helix: 1.93 (0.15), residues: 1124 sheet: 1.13 (0.32), residues: 252 loop : 0.23 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 44 TYR 0.015 0.002 TYR D 497 PHE 0.019 0.002 PHE A 474 TRP 0.009 0.001 TRP B 491 HIS 0.007 0.002 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (15712) covalent geometry : angle 0.58566 / 0.31 (21332) hydrogen bonds : bond 0.06118 / 4.04 ( 1052) hydrogen bonds : angle 5.12152 / 3.66 ( 3216) link_BETA1-4 : bond 0.00235 / 0.12 ( 4) link_BETA1-4 : angle 1.85441 / 0.97 ( 12) link_NAG-ASN : bond 0.00147 / 0.07 ( 4) link_NAG-ASN : angle 2.68812 / 1.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 140 time to evaluate : 0.604 Fit side-chains REVERT: A 44 ARG cc_start: 0.5856 (ptm160) cc_final: 0.5547 (mtm-85) REVERT: A 65 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7190 (mtmp) REVERT: A 95 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: A 276 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: A 358 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7959 (mp) REVERT: B 44 ARG cc_start: 0.5864 (ptm160) cc_final: 0.5552 (mtm-85) REVERT: B 65 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7029 (ttmt) REVERT: B 95 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: B 115 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: B 276 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: B 358 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7973 (mp) REVERT: C 44 ARG cc_start: 0.5880 (ptm160) cc_final: 0.5615 (mtm-85) REVERT: C 65 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7024 (ttmt) REVERT: C 95 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: C 276 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: C 303 VAL cc_start: 0.7605 (t) cc_final: 0.7394 (p) REVERT: C 358 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7989 (mp) REVERT: D 44 ARG cc_start: 0.5846 (ptm160) cc_final: 0.5428 (mtm-85) REVERT: D 65 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7218 (mtmp) REVERT: D 95 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: D 276 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: D 358 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7952 (mp) outliers start: 63 outliers final: 25 residues processed: 182 average time/residue: 0.5421 time to fit residues: 109.4962 Evaluate side-chains 160 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 79 optimal weight: 5.9990 chunk 180 optimal weight: 0.0270 chunk 121 optimal weight: 0.0070 chunk 19 optimal weight: 0.0060 chunk 33 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.0076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 ASN B 247 ASN B 327 GLN C 247 ASN D 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.097610 restraints weight = 15605.242| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.80 r_work: 0.2841 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15720 Z= 0.119 Angle : 0.495 6.084 21356 Z= 0.257 Chirality : 0.039 0.126 2460 Planarity : 0.004 0.054 2600 Dihedral : 6.434 53.240 2316 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.15 % Allowed : 15.55 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.20), residues: 1844 helix: 2.30 (0.15), residues: 1112 sheet: 1.20 (0.31), residues: 252 loop : 0.46 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 42 TYR 0.013 0.001 TYR C 497 PHE 0.011 0.001 PHE A 474 TRP 0.006 0.001 TRP D 491 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (15712) covalent geometry : angle 0.49239 / 0.26 (21332) hydrogen bonds : bond 0.04799 / 3.16 ( 1052) hydrogen bonds : angle 4.71593 / 3.38 ( 3216) link_BETA1-4 : bond 0.00081 / 0.04 ( 4) link_BETA1-4 : angle 1.89585 / 1.00 ( 12) link_NAG-ASN : bond 0.00017 / 0.01 ( 4) link_NAG-ASN : angle 1.47210 / 0.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.761 Fit side-chains REVERT: A 44 ARG cc_start: 0.5870 (ptm160) cc_final: 0.5563 (mtm-85) REVERT: A 65 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6942 (ttmt) REVERT: A 95 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: A 358 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7920 (mp) REVERT: B 44 ARG cc_start: 0.5865 (ptm160) cc_final: 0.5555 (mtm-85) REVERT: B 65 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6997 (ttmt) REVERT: B 95 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: B 358 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7943 (mp) REVERT: C 44 ARG cc_start: 0.5891 (ptm160) cc_final: 0.5496 (mtm-85) REVERT: C 65 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6983 (ttmt) REVERT: C 95 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: C 358 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7943 (mp) REVERT: D 44 ARG cc_start: 0.5865 (ptm160) cc_final: 0.5608 (mtm-85) REVERT: D 65 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6926 (ttmt) REVERT: D 95 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: D 358 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7923 (mp) outliers start: 36 outliers final: 7 residues processed: 173 average time/residue: 0.5790 time to fit residues: 110.7278 Evaluate side-chains 158 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 183 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 ASN A 327 GLN B 247 ASN B 327 GLN C 247 ASN C 327 GLN D 247 ASN D 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.136885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.094690 restraints weight = 15578.119| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.78 r_work: 0.2795 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15720 Z= 0.195 Angle : 0.575 6.085 21356 Z= 0.304 Chirality : 0.042 0.129 2460 Planarity : 0.005 0.036 2600 Dihedral : 6.586 54.285 2316 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.35 % Allowed : 14.11 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.20), residues: 1844 helix: 2.14 (0.15), residues: 1124 sheet: 1.17 (0.31), residues: 252 loop : 0.39 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 347 TYR 0.015 0.002 TYR A 497 PHE 0.019 0.002 PHE C 474 TRP 0.009 0.001 TRP B 491 HIS 0.007 0.002 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (15712) covalent geometry : angle 0.57084 / 0.30 (21332) hydrogen bonds : bond 0.05837 / 3.85 ( 1052) hydrogen bonds : angle 5.00111 / 3.58 ( 3216) link_BETA1-4 : bond 0.00214 / 0.11 ( 4) link_BETA1-4 : angle 1.94427 / 1.02 ( 12) link_NAG-ASN : bond 0.00145 / 0.07 ( 4) link_NAG-ASN : angle 2.43724 / 1.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 0.598 Fit side-chains REVERT: A 44 ARG cc_start: 0.5895 (ptm160) cc_final: 0.5449 (ptp90) REVERT: A 65 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7026 (ttmt) REVERT: A 95 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: A 358 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7964 (mp) REVERT: B 44 ARG cc_start: 0.5867 (ptm160) cc_final: 0.5463 (ptp90) REVERT: B 65 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7062 (ttmt) REVERT: B 95 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: B 115 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7889 (m-30) REVERT: B 358 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7992 (mp) REVERT: C 65 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7020 (ttmt) REVERT: C 95 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: C 358 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8002 (mp) REVERT: D 44 ARG cc_start: 0.5809 (ptm160) cc_final: 0.5503 (mtm-85) REVERT: D 65 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7083 (ttmt) REVERT: D 95 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: D 115 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: D 358 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7981 (mp) outliers start: 56 outliers final: 18 residues processed: 177 average time/residue: 0.5881 time to fit residues: 114.9710 Evaluate side-chains 159 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 151 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 ASN A 327 GLN B 247 ASN B 327 GLN C 247 ASN C 327 GLN D 247 ASN D 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.094046 restraints weight = 15478.712| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.73 r_work: 0.2780 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15720 Z= 0.223 Angle : 0.611 6.165 21356 Z= 0.323 Chirality : 0.044 0.131 2460 Planarity : 0.005 0.038 2600 Dihedral : 6.774 54.232 2316 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.59 % Allowed : 13.64 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.19), residues: 1844 helix: 1.96 (0.15), residues: 1124 sheet: 1.14 (0.31), residues: 252 loop : 0.24 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 347 TYR 0.017 0.002 TYR D 404 PHE 0.021 0.003 PHE B 474 TRP 0.009 0.001 TRP C 491 HIS 0.009 0.002 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (15712) covalent geometry : angle 0.60603 / 0.32 (21332) hydrogen bonds : bond 0.06210 / 4.10 ( 1052) hydrogen bonds : angle 5.15749 / 3.69 ( 3216) link_BETA1-4 : bond 0.00343 / 0.17 ( 4) link_BETA1-4 : angle 1.97096 / 1.04 ( 12) link_NAG-ASN : bond 0.00165 / 0.08 ( 4) link_NAG-ASN : angle 2.64816 / 1.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 125 time to evaluate : 0.632 Fit side-chains REVERT: A 44 ARG cc_start: 0.5881 (ptm160) cc_final: 0.5558 (mtm-85) REVERT: A 65 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7064 (mtmm) REVERT: A 95 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: A 358 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7991 (mp) REVERT: B 44 ARG cc_start: 0.5878 (ptm160) cc_final: 0.5550 (mtm-85) REVERT: B 65 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7164 (mtmm) REVERT: B 95 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: B 115 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: B 276 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: B 358 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8017 (mp) REVERT: C 44 ARG cc_start: 0.5870 (OUTLIER) cc_final: 0.5398 (mtm-85) REVERT: C 65 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7068 (mtmm) REVERT: C 95 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: C 303 VAL cc_start: 0.7575 (t) cc_final: 0.7353 (p) REVERT: C 358 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8028 (mp) REVERT: D 65 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7045 (mtmm) REVERT: D 95 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: D 115 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: D 358 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8002 (mp) outliers start: 60 outliers final: 27 residues processed: 178 average time/residue: 0.5618 time to fit residues: 111.0354 Evaluate side-chains 164 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 32 optimal weight: 0.4980 chunk 46 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 ASN A 327 GLN B 247 ASN B 327 GLN C 247 ASN C 327 GLN D 247 ASN D 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.090405 restraints weight = 15633.973| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.46 r_work: 0.2850 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15720 Z= 0.218 Angle : 0.606 6.142 21356 Z= 0.321 Chirality : 0.044 0.131 2460 Planarity : 0.005 0.037 2600 Dihedral : 6.756 54.301 2316 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.29 % Allowed : 13.70 % Favored : 83.01 % 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: 2.04 (0.19), residues: 1844 helix: 1.92 (0.15), residues: 1124 sheet: 1.10 (0.31), residues: 252 loop : 0.23 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 347 TYR 0.016 0.002 TYR A 404 PHE 0.020 0.002 PHE B 474 TRP 0.009 0.001 TRP C 491 HIS 0.008 0.002 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (15712) covalent geometry : angle 0.60073 / 0.32 (21332) hydrogen bonds : bond 0.06120 / 4.04 ( 1052) hydrogen bonds : angle 5.15381 / 3.69 ( 3216) link_BETA1-4 : bond 0.00393 / 0.20 ( 4) link_BETA1-4 : angle 2.07494 / 1.12 ( 12) link_NAG-ASN : bond 0.00203 / 0.10 ( 4) link_NAG-ASN : angle 2.63156 / 1.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 128 time to evaluate : 0.641 Fit side-chains REVERT: A 65 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7172 (mtmp) REVERT: A 95 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: A 355 TYR cc_start: 0.8472 (m-10) cc_final: 0.8240 (m-10) REVERT: A 358 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7974 (mp) REVERT: B 65 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7174 (mtmp) REVERT: B 95 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: B 115 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7767 (m-30) REVERT: B 276 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: B 355 TYR cc_start: 0.8464 (m-10) cc_final: 0.8221 (m-10) REVERT: B 358 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7981 (mp) REVERT: C 44 ARG cc_start: 0.5881 (OUTLIER) cc_final: 0.5465 (mtm-85) REVERT: C 65 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7172 (mtmp) REVERT: C 95 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: C 303 VAL cc_start: 0.7551 (t) cc_final: 0.7340 (p) REVERT: C 355 TYR cc_start: 0.8462 (m-10) cc_final: 0.8218 (m-10) REVERT: C 358 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7985 (mp) REVERT: D 44 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.5432 (mtm-85) REVERT: D 65 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7142 (mtmm) REVERT: D 95 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: D 358 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8003 (mp) outliers start: 55 outliers final: 25 residues processed: 176 average time/residue: 0.5187 time to fit residues: 101.4852 Evaluate side-chains 165 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 53 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN B 327 GLN C 327 GLN D 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.090753 restraints weight = 15612.546| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.45 r_work: 0.2845 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15720 Z= 0.201 Angle : 0.589 6.148 21356 Z= 0.312 Chirality : 0.043 0.129 2460 Planarity : 0.005 0.037 2600 Dihedral : 6.740 54.292 2316 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.69 % Allowed : 14.23 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.19), residues: 1844 helix: 1.95 (0.15), residues: 1124 sheet: 1.14 (0.31), residues: 252 loop : 0.23 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 44 TYR 0.016 0.002 TYR D 355 PHE 0.019 0.002 PHE B 474 TRP 0.009 0.001 TRP C 491 HIS 0.008 0.002 HIS C 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (15712) covalent geometry : angle 0.58446 / 0.31 (21332) hydrogen bonds : bond 0.05972 / 3.94 ( 1052) hydrogen bonds : angle 5.11275 / 3.66 ( 3216) link_BETA1-4 : bond 0.00338 / 0.17 ( 4) link_BETA1-4 : angle 2.05845 / 1.11 ( 12) link_NAG-ASN : bond 0.00177 / 0.09 ( 4) link_NAG-ASN : angle 2.57512 / 1.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.539 Fit side-chains REVERT: A 44 ARG cc_start: 0.5857 (ptm-80) cc_final: 0.5358 (mtm-85) REVERT: A 65 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7196 (mtmp) REVERT: A 95 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: A 358 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7966 (mp) REVERT: B 44 ARG cc_start: 0.5858 (ptm-80) cc_final: 0.5354 (mtm-85) REVERT: B 65 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7213 (mtmp) REVERT: B 95 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: B 115 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7797 (m-30) REVERT: B 276 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: B 358 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7973 (mp) REVERT: C 65 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7222 (mtmp) REVERT: C 95 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: C 358 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7999 (mp) REVERT: D 65 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7103 (mtmm) REVERT: D 95 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: D 358 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7977 (mp) outliers start: 45 outliers final: 24 residues processed: 168 average time/residue: 0.5112 time to fit residues: 95.8833 Evaluate side-chains 164 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 34 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.138645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.093109 restraints weight = 15599.526| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.49 r_work: 0.2889 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15720 Z= 0.133 Angle : 0.523 6.087 21356 Z= 0.272 Chirality : 0.040 0.126 2460 Planarity : 0.004 0.035 2600 Dihedral : 6.521 53.392 2316 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.85 % Allowed : 15.37 % Favored : 82.78 % 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: 2.43 (0.19), residues: 1844 helix: 2.25 (0.15), residues: 1112 sheet: 1.20 (0.31), residues: 252 loop : 0.38 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 44 TYR 0.013 0.001 TYR A 404 PHE 0.013 0.002 PHE B 474 TRP 0.007 0.001 TRP D 354 HIS 0.004 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (15712) covalent geometry : angle 0.51878 / 0.27 (21332) hydrogen bonds : bond 0.05002 / 3.30 ( 1052) hydrogen bonds : angle 4.82361 / 3.46 ( 3216) link_BETA1-4 : bond 0.00053 / 0.03 ( 4) link_BETA1-4 : angle 2.07114 / 1.12 ( 12) link_NAG-ASN : bond 0.00012 / 0.01 ( 4) link_NAG-ASN : angle 1.81623 / 1.02 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.600 Fit side-chains REVERT: A 44 ARG cc_start: 0.5909 (OUTLIER) cc_final: 0.5366 (mtm-85) REVERT: A 65 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.6937 (ttmt) REVERT: A 95 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: A 358 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7860 (mp) REVERT: B 44 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.5342 (mtm-85) REVERT: B 65 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7073 (mtmm) REVERT: B 95 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: B 276 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: B 358 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7893 (mp) REVERT: C 65 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7081 (mtmm) REVERT: C 95 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: C 358 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7898 (mp) REVERT: D 65 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6922 (ttmt) REVERT: D 95 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: D 358 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7887 (mp) outliers start: 31 outliers final: 14 residues processed: 166 average time/residue: 0.4873 time to fit residues: 90.9394 Evaluate side-chains 159 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 102 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.136959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.091433 restraints weight = 15513.904| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.45 r_work: 0.2862 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15720 Z= 0.178 Angle : 0.571 6.117 21356 Z= 0.301 Chirality : 0.042 0.126 2460 Planarity : 0.004 0.037 2600 Dihedral : 6.606 54.320 2316 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.03 % Allowed : 15.01 % Favored : 82.95 % 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: 2.32 (0.19), residues: 1844 helix: 2.14 (0.15), residues: 1124 sheet: 1.16 (0.31), residues: 252 loop : 0.37 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.016 0.002 TYR D 404 PHE 0.018 0.002 PHE B 474 TRP 0.009 0.001 TRP C 491 HIS 0.006 0.002 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (15712) covalent geometry : angle 0.56584 / 0.30 (21332) hydrogen bonds : bond 0.05660 / 3.74 ( 1052) hydrogen bonds : angle 4.99024 / 3.58 ( 3216) link_BETA1-4 : bond 0.00227 / 0.11 ( 4) link_BETA1-4 : angle 2.06055 / 1.12 ( 12) link_NAG-ASN : bond 0.00140 / 0.07 ( 4) link_NAG-ASN : angle 2.42510 / 1.35 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5608.48 seconds wall clock time: 96 minutes 21.68 seconds (5781.68 seconds total)