Starting phenix.real_space_refine on Wed Jul 30 09:47:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5y_45237/07_2025/9c5y_45237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5y_45237/07_2025/9c5y_45237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c5y_45237/07_2025/9c5y_45237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5y_45237/07_2025/9c5y_45237.map" model { file = "/net/cci-nas-00/data/ceres_data/9c5y_45237/07_2025/9c5y_45237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5y_45237/07_2025/9c5y_45237.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.048 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 7844 2.51 5 N 2083 2.21 5 O 2307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12302 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "B" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "C" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3051 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "A" 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: "B" 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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 Time building chain proxies: 8.13, per 1000 atoms: 0.66 Number of scatterers: 12302 At special positions: 0 Unit cell: (102.82, 157.94, 92.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2307 8.00 N 2083 7.00 C 7844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 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 NAG-ASN " NAG A1001 " - " ASN A 275 " " NAG A1002 " - " ASN A 412 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 412 " " NAG C1001 " - " ASN C 412 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 1.8 seconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 18 sheets defined 41.3% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.735A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'A' and resid 179 through 185 removed outlier: 3.874A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.998A pdb=" N ARG A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 removed outlier: 3.539A pdb=" N ARG A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 246 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.554A pdb=" N GLN A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 365 Processing helix chain 'B' and resid 51 through 66 Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.553A pdb=" N LEU B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.577A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.936A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.890A pdb=" N ILE B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.575A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 266 through 271 removed outlier: 4.592A pdb=" N TYR B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 300 Processing helix chain 'B' and resid 317 through 336 Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'C' and resid 51 through 65 removed outlier: 3.559A pdb=" N ASN C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.780A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 167 Processing helix chain 'C' and resid 179 through 185 removed outlier: 4.055A pdb=" N ILE C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 211 through 222 Processing helix chain 'C' and resid 231 through 245 Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.515A pdb=" N TYR C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 306 through 310 removed outlier: 4.508A pdb=" N GLY C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.928A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 101 removed outlier: 3.503A pdb=" N LEU D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 155 through 167 Processing helix chain 'D' and resid 178 through 182 removed outlier: 3.612A pdb=" N LEU D 182 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 190 through 195 removed outlier: 4.264A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 245 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 266 through 271 removed outlier: 4.852A pdb=" N TYR D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 4.010A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 Processing helix chain 'D' and resid 355 through 365 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 83 removed outlier: 6.960A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLN A 81 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 105 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N HIS A 129 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU A 149 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLN A 131 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ARG A 384 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N SER A 148 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 203 removed outlier: 7.108A pdb=" N VAL A 172 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR A 171 " --> pdb=" O HIS A 225 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ILE A 227 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N PHE A 279 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE A 256 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 389 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR A 404 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 404 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.536A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 35 through 43 removed outlier: 3.633A pdb=" N GLY B 40 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.268A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.664A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 254 " --> pdb=" O ASN B 275 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 367 through 370 removed outlier: 3.512A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 392 through 395 Processing sheet with id=AA9, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 83 removed outlier: 3.655A pdb=" N THR C 77 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N PHE C 107 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLY C 39 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ARG C 384 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N SER C 148 " --> pdb=" O ARG C 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 198 through 199 removed outlier: 7.507A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 198 through 199 removed outlier: 6.782A pdb=" N THR C 171 " --> pdb=" O HIS C 225 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE C 227 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 277 through 278 Processing sheet with id=AB5, first strand: chain 'C' and resid 369 through 370 Processing sheet with id=AB6, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AB7, first strand: chain 'D' and resid 77 through 83 removed outlier: 3.999A pdb=" N GLY D 40 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ARG D 37 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N PHE D 107 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLY D 39 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 202 through 203 removed outlier: 5.977A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASP D 229 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL D 175 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU D 389 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR D 404 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 367 through 370 removed outlier: 3.645A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1395 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: 3.95 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3955 1.34 - 1.46: 2721 1.46 - 1.58: 5786 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 12582 Sorted by residual: bond pdb=" C1 NAG D1001 " pdb=" O5 NAG D1001 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG D1002 " pdb=" O5 NAG D1002 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG C1001 " pdb=" O5 NAG C1001 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.72e+00 bond pdb=" C1 NAG A1002 " pdb=" O5 NAG A1002 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.69e+00 ... (remaining 12577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 16544 1.31 - 2.61: 380 2.61 - 3.92: 86 3.92 - 5.22: 21 5.22 - 6.53: 6 Bond angle restraints: 17037 Sorted by residual: angle pdb=" CA MET C 340 " pdb=" CB MET C 340 " pdb=" CG MET C 340 " ideal model delta sigma weight residual 114.10 119.67 -5.57 2.00e+00 2.50e-01 7.76e+00 angle pdb=" C ILE B 64 " pdb=" N ASN B 65 " pdb=" CA ASN B 65 " ideal model delta sigma weight residual 121.58 116.20 5.38 1.95e+00 2.63e-01 7.61e+00 angle pdb=" N GLY A 370 " pdb=" CA GLY A 370 " pdb=" C GLY A 370 " ideal model delta sigma weight residual 111.20 114.99 -3.79 1.39e+00 5.18e-01 7.44e+00 angle pdb=" N GLN B 241 " pdb=" CA GLN B 241 " pdb=" CB GLN B 241 " ideal model delta sigma weight residual 110.28 114.04 -3.76 1.55e+00 4.16e-01 5.88e+00 angle pdb=" N GLN C 241 " pdb=" CA GLN C 241 " pdb=" CB GLN C 241 " ideal model delta sigma weight residual 110.28 114.03 -3.75 1.55e+00 4.16e-01 5.87e+00 ... (remaining 17032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 6754 17.27 - 34.55: 697 34.55 - 51.82: 142 51.82 - 69.09: 29 69.09 - 86.37: 5 Dihedral angle restraints: 7627 sinusoidal: 3159 harmonic: 4468 Sorted by residual: dihedral pdb=" CA PHE C 153 " pdb=" C PHE C 153 " pdb=" N SER C 154 " pdb=" CA SER C 154 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA PHE B 107 " pdb=" C PHE B 107 " pdb=" N GLY B 108 " pdb=" CA GLY B 108 " ideal model delta harmonic sigma weight residual 180.00 -161.51 -18.49 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CB CYS B 96 " pdb=" SG CYS B 96 " pdb=" SG CYS B 347 " pdb=" CB CYS B 347 " ideal model delta sinusoidal sigma weight residual -86.00 -116.30 30.30 1 1.00e+01 1.00e-02 1.31e+01 ... (remaining 7624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1769 0.077 - 0.153: 147 0.153 - 0.230: 1 0.230 - 0.306: 1 0.306 - 0.383: 1 Chirality restraints: 1919 Sorted by residual: chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 275 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C1 NAG D1001 " pdb=" ND2 ASN D 275 " pdb=" C2 NAG D1001 " pdb=" O5 NAG D1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB VAL B 266 " pdb=" CA VAL B 266 " pdb=" CG1 VAL B 266 " pdb=" CG2 VAL B 266 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 1916 not shown) Planarity restraints: 2170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 191 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO B 192 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 340 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C MET C 340 " 0.026 2.00e-02 2.50e+03 pdb=" O MET C 340 " -0.010 2.00e-02 2.50e+03 pdb=" N THR C 341 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 267 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 268 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " 0.020 5.00e-02 4.00e+02 ... (remaining 2167 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1171 2.75 - 3.28: 12155 3.28 - 3.82: 20937 3.82 - 4.36: 24578 4.36 - 4.90: 43815 Nonbonded interactions: 102656 Sorted by model distance: nonbonded pdb=" OE1 GLN A 165 " pdb=" OH TYR A 195 " model vdw 2.207 3.040 nonbonded pdb=" O SER B 100 " pdb=" OG SER B 344 " model vdw 2.278 3.040 nonbonded pdb=" OD1 ASP A 319 " pdb=" N ALA A 320 " model vdw 2.285 3.120 nonbonded pdb=" ND2 ASN B 123 " pdb=" OD1 ASP B 143 " model vdw 2.286 3.120 nonbonded pdb=" OG1 THR C 317 " pdb=" OD1 ASP C 319 " model vdw 2.292 3.040 ... (remaining 102651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 415 or resid 1001)) selection = (chain 'B' and (resid 33 through 415 or resid 1001)) selection = chain 'C' selection = (chain 'D' and (resid 33 through 415 or resid 1001)) } 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: 2.020 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.010 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:5.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.003 0.045 12593 Z= 0.143 Angle : 0.535 11.300 17066 Z= 0.269 Chirality : 0.041 0.383 1919 Planarity : 0.004 0.047 2163 Dihedral : 14.270 86.366 4727 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1524 helix: 1.53 (0.22), residues: 588 sheet: -2.14 (0.38), residues: 188 loop : -1.33 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 296 HIS 0.003 0.001 HIS C 328 PHE 0.017 0.001 PHE A 337 TYR 0.018 0.001 TYR C 252 ARG 0.008 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 7) link_NAG-ASN : angle 3.68272 ( 21) hydrogen bonds : bond 0.12862 ( 487) hydrogen bonds : angle 5.61834 ( 1395) SS BOND : bond 0.00145 ( 4) SS BOND : angle 0.48094 ( 8) covalent geometry : bond 0.00332 (12582) covalent geometry : angle 0.51974 (17037) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7650 (mp) cc_final: 0.7277 (pt) REVERT: A 79 ASP cc_start: 0.6173 (t0) cc_final: 0.5899 (t0) REVERT: A 234 MET cc_start: 0.7308 (ttp) cc_final: 0.6949 (ttp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2343 time to fit residues: 66.6930 Evaluate side-chains 166 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN C 165 GLN C 348 ASN D 116 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.149586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114625 restraints weight = 15209.642| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.48 r_work: 0.3161 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12593 Z= 0.202 Angle : 0.562 11.554 17066 Z= 0.286 Chirality : 0.043 0.437 1919 Planarity : 0.004 0.047 2163 Dihedral : 5.290 56.472 1803 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.19 % Allowed : 8.21 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1524 helix: 1.48 (0.22), residues: 588 sheet: -1.66 (0.31), residues: 292 loop : -1.55 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 296 HIS 0.004 0.001 HIS C 328 PHE 0.035 0.001 PHE A 337 TYR 0.025 0.002 TYR C 324 ARG 0.005 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 7) link_NAG-ASN : angle 3.77694 ( 21) hydrogen bonds : bond 0.03877 ( 487) hydrogen bonds : angle 4.43166 ( 1395) SS BOND : bond 0.00164 ( 4) SS BOND : angle 0.41692 ( 8) covalent geometry : bond 0.00489 (12582) covalent geometry : angle 0.54676 (17037) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7706 (mp) cc_final: 0.7067 (pt) REVERT: A 79 ASP cc_start: 0.6886 (t0) cc_final: 0.6556 (t0) REVERT: A 229 ASP cc_start: 0.8213 (t0) cc_final: 0.7964 (t0) REVERT: A 340 MET cc_start: 0.6349 (mtp) cc_final: 0.5872 (ttm) REVERT: B 64 ILE cc_start: 0.8655 (mp) cc_final: 0.8395 (mp) REVERT: B 412 ASN cc_start: 0.8779 (t0) cc_final: 0.8519 (t0) REVERT: C 55 LEU cc_start: 0.7339 (mt) cc_final: 0.7050 (mt) REVERT: C 86 TYR cc_start: 0.7880 (m-80) cc_final: 0.7680 (m-80) REVERT: C 210 ASP cc_start: 0.7467 (m-30) cc_final: 0.7247 (p0) REVERT: C 337 PHE cc_start: 0.7831 (t80) cc_final: 0.7535 (t80) REVERT: C 379 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8286 (tptp) outliers start: 16 outliers final: 11 residues processed: 181 average time/residue: 0.2853 time to fit residues: 75.7724 Evaluate side-chains 174 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 380 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 71 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 150 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.151725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118002 restraints weight = 15371.608| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.43 r_work: 0.3202 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12593 Z= 0.117 Angle : 0.487 10.815 17066 Z= 0.247 Chirality : 0.041 0.429 1919 Planarity : 0.004 0.045 2163 Dihedral : 4.985 59.766 1803 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.72 % Allowed : 11.04 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1524 helix: 1.71 (0.22), residues: 588 sheet: -1.73 (0.32), residues: 276 loop : -1.46 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.003 0.001 HIS A 253 PHE 0.032 0.001 PHE A 337 TYR 0.020 0.001 TYR C 324 ARG 0.004 0.000 ARG A 358 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 7) link_NAG-ASN : angle 3.51861 ( 21) hydrogen bonds : bond 0.03321 ( 487) hydrogen bonds : angle 4.18649 ( 1395) SS BOND : bond 0.00115 ( 4) SS BOND : angle 0.44901 ( 8) covalent geometry : bond 0.00275 (12582) covalent geometry : angle 0.47140 (17037) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7707 (mp) cc_final: 0.7073 (pt) REVERT: A 79 ASP cc_start: 0.6827 (t0) cc_final: 0.6437 (t0) REVERT: A 84 ASN cc_start: 0.8046 (m110) cc_final: 0.7197 (t0) REVERT: C 55 LEU cc_start: 0.7325 (mt) cc_final: 0.7059 (mt) REVERT: C 86 TYR cc_start: 0.7858 (m-80) cc_final: 0.7646 (m-80) REVERT: C 379 LYS cc_start: 0.8425 (mmmt) cc_final: 0.8198 (tptp) outliers start: 23 outliers final: 17 residues processed: 182 average time/residue: 0.2340 time to fit residues: 62.8078 Evaluate side-chains 184 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 147 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 81 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 136 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116306 restraints weight = 15122.218| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.44 r_work: 0.3190 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12593 Z= 0.132 Angle : 0.491 10.824 17066 Z= 0.249 Chirality : 0.041 0.419 1919 Planarity : 0.004 0.044 2163 Dihedral : 4.838 56.275 1803 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.01 % Allowed : 12.69 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1524 helix: 1.76 (0.22), residues: 588 sheet: -1.73 (0.33), residues: 268 loop : -1.47 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.003 0.001 HIS C 253 PHE 0.031 0.001 PHE A 337 TYR 0.019 0.001 TYR D 44 ARG 0.003 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00645 ( 7) link_NAG-ASN : angle 3.48161 ( 21) hydrogen bonds : bond 0.03274 ( 487) hydrogen bonds : angle 4.10186 ( 1395) SS BOND : bond 0.00135 ( 4) SS BOND : angle 0.42150 ( 8) covalent geometry : bond 0.00316 (12582) covalent geometry : angle 0.47603 (17037) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7764 (mp) cc_final: 0.7291 (pt) REVERT: A 79 ASP cc_start: 0.6822 (t0) cc_final: 0.6452 (t0) REVERT: A 84 ASN cc_start: 0.8121 (m110) cc_final: 0.7205 (t0) REVERT: B 156 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7819 (mt) REVERT: C 55 LEU cc_start: 0.7372 (mt) cc_final: 0.6939 (mt) REVERT: C 149 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8400 (mp) REVERT: C 210 ASP cc_start: 0.7566 (m-30) cc_final: 0.7174 (p0) REVERT: C 379 LYS cc_start: 0.8419 (mmmt) cc_final: 0.8192 (tptp) outliers start: 27 outliers final: 19 residues processed: 187 average time/residue: 0.2477 time to fit residues: 67.7970 Evaluate side-chains 176 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 360 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.147057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112070 restraints weight = 15312.247| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.46 r_work: 0.3124 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12593 Z= 0.234 Angle : 0.566 12.326 17066 Z= 0.286 Chirality : 0.043 0.447 1919 Planarity : 0.004 0.044 2163 Dihedral : 4.927 54.418 1803 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.76 % Allowed : 13.21 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.22), residues: 1524 helix: 1.47 (0.22), residues: 588 sheet: -1.87 (0.32), residues: 268 loop : -1.54 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.006 0.001 HIS B 328 PHE 0.027 0.002 PHE A 337 TYR 0.019 0.002 TYR D 44 ARG 0.004 0.000 ARG A 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 7) link_NAG-ASN : angle 3.83580 ( 21) hydrogen bonds : bond 0.03789 ( 487) hydrogen bonds : angle 4.23942 ( 1395) SS BOND : bond 0.00220 ( 4) SS BOND : angle 0.58956 ( 8) covalent geometry : bond 0.00566 (12582) covalent geometry : angle 0.55058 (17037) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7917 (mp) cc_final: 0.7347 (pt) REVERT: A 79 ASP cc_start: 0.7001 (t0) cc_final: 0.6599 (t0) REVERT: A 84 ASN cc_start: 0.8329 (m110) cc_final: 0.7392 (t0) REVERT: A 229 ASP cc_start: 0.8226 (t0) cc_final: 0.7967 (t0) REVERT: B 156 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7842 (mt) REVERT: C 149 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8493 (mp) REVERT: C 210 ASP cc_start: 0.7622 (m-30) cc_final: 0.7304 (p0) REVERT: C 288 GLN cc_start: 0.7631 (mp10) cc_final: 0.7388 (mp10) REVERT: C 379 LYS cc_start: 0.8537 (mmmt) cc_final: 0.8309 (tptp) REVERT: C 415 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.4808 (tp30) REVERT: D 68 ARG cc_start: 0.7898 (mmp80) cc_final: 0.7544 (mmp80) REVERT: D 337 PHE cc_start: 0.8582 (t80) cc_final: 0.8144 (t80) outliers start: 37 outliers final: 24 residues processed: 192 average time/residue: 0.3225 time to fit residues: 95.6145 Evaluate side-chains 185 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 380 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 84 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.148851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114071 restraints weight = 15464.588| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.45 r_work: 0.3139 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12593 Z= 0.157 Angle : 0.517 11.942 17066 Z= 0.260 Chirality : 0.042 0.443 1919 Planarity : 0.004 0.044 2163 Dihedral : 4.721 54.459 1803 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.61 % Allowed : 14.18 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.22), residues: 1524 helix: 1.55 (0.22), residues: 596 sheet: -1.87 (0.33), residues: 268 loop : -1.47 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.006 0.001 HIS B 328 PHE 0.024 0.001 PHE A 337 TYR 0.020 0.001 TYR D 44 ARG 0.002 0.000 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00721 ( 7) link_NAG-ASN : angle 3.87580 ( 21) hydrogen bonds : bond 0.03444 ( 487) hydrogen bonds : angle 4.12963 ( 1395) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.50265 ( 8) covalent geometry : bond 0.00379 (12582) covalent geometry : angle 0.49883 (17037) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7931 (mp) cc_final: 0.7383 (pt) REVERT: A 84 ASN cc_start: 0.8290 (m110) cc_final: 0.7409 (t0) REVERT: A 153 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: A 229 ASP cc_start: 0.8130 (t0) cc_final: 0.7883 (t0) REVERT: B 156 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7879 (mt) REVERT: C 149 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8462 (mp) REVERT: C 210 ASP cc_start: 0.7598 (m-30) cc_final: 0.7295 (p0) REVERT: C 288 GLN cc_start: 0.7646 (mp10) cc_final: 0.7395 (mp10) REVERT: C 379 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8202 (tptp) REVERT: C 415 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.4739 (tp30) REVERT: D 68 ARG cc_start: 0.7932 (mmp80) cc_final: 0.7616 (mmp80) REVERT: D 337 PHE cc_start: 0.8447 (t80) cc_final: 0.7849 (t80) outliers start: 35 outliers final: 24 residues processed: 185 average time/residue: 0.2826 time to fit residues: 77.3200 Evaluate side-chains 184 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 138 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.0030 chunk 34 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN D 136 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.150193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116701 restraints weight = 15193.753| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.38 r_work: 0.3191 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12593 Z= 0.108 Angle : 0.477 10.997 17066 Z= 0.240 Chirality : 0.041 0.420 1919 Planarity : 0.003 0.043 2163 Dihedral : 4.475 54.154 1803 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.46 % Allowed : 15.15 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1524 helix: 1.74 (0.22), residues: 596 sheet: -1.76 (0.33), residues: 268 loop : -1.36 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.005 0.001 HIS B 328 PHE 0.023 0.001 PHE A 337 TYR 0.020 0.001 TYR D 44 ARG 0.005 0.000 ARG A 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 7) link_NAG-ASN : angle 3.53126 ( 21) hydrogen bonds : bond 0.03110 ( 487) hydrogen bonds : angle 4.03972 ( 1395) SS BOND : bond 0.00122 ( 4) SS BOND : angle 0.41057 ( 8) covalent geometry : bond 0.00255 (12582) covalent geometry : angle 0.46049 (17037) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7866 (mp) cc_final: 0.7290 (pt) REVERT: A 79 ASP cc_start: 0.6774 (t0) cc_final: 0.6306 (t0) REVERT: A 84 ASN cc_start: 0.8203 (m110) cc_final: 0.7450 (t0) REVERT: A 153 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7297 (m-80) REVERT: A 229 ASP cc_start: 0.8075 (t0) cc_final: 0.7862 (t0) REVERT: C 210 ASP cc_start: 0.7557 (m-30) cc_final: 0.7184 (p0) REVERT: C 241 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7508 (mt0) REVERT: C 288 GLN cc_start: 0.7577 (mp10) cc_final: 0.7330 (mp10) REVERT: C 337 PHE cc_start: 0.7921 (t80) cc_final: 0.7603 (t80) REVERT: C 415 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.4582 (tp30) REVERT: D 68 ARG cc_start: 0.7944 (mmp80) cc_final: 0.7637 (mmp80) REVERT: D 337 PHE cc_start: 0.8440 (t80) cc_final: 0.8022 (t80) outliers start: 33 outliers final: 21 residues processed: 197 average time/residue: 0.2485 time to fit residues: 73.1958 Evaluate side-chains 187 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 150 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 136 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114244 restraints weight = 15337.893| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.39 r_work: 0.3151 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12593 Z= 0.164 Angle : 0.524 11.503 17066 Z= 0.263 Chirality : 0.042 0.425 1919 Planarity : 0.004 0.042 2163 Dihedral : 4.536 54.669 1803 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.24 % Allowed : 15.60 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1524 helix: 1.68 (0.22), residues: 596 sheet: -1.79 (0.32), residues: 276 loop : -1.39 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.005 0.001 HIS B 328 PHE 0.025 0.001 PHE A 337 TYR 0.019 0.001 TYR D 44 ARG 0.004 0.000 ARG A 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 7) link_NAG-ASN : angle 3.62183 ( 21) hydrogen bonds : bond 0.03400 ( 487) hydrogen bonds : angle 4.10542 ( 1395) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.48103 ( 8) covalent geometry : bond 0.00395 (12582) covalent geometry : angle 0.50903 (17037) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8608 (ttm) cc_final: 0.8407 (ttt) REVERT: A 70 LEU cc_start: 0.7917 (mp) cc_final: 0.7297 (pt) REVERT: A 79 ASP cc_start: 0.6567 (t0) cc_final: 0.6345 (t0) REVERT: A 84 ASN cc_start: 0.8328 (m110) cc_final: 0.7468 (t0) REVERT: A 153 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7314 (m-80) REVERT: A 229 ASP cc_start: 0.8127 (t0) cc_final: 0.7891 (t0) REVERT: B 359 PHE cc_start: 0.8033 (t80) cc_final: 0.7809 (t80) REVERT: C 210 ASP cc_start: 0.7558 (m-30) cc_final: 0.7204 (p0) REVERT: C 241 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7510 (mt0) REVERT: C 288 GLN cc_start: 0.7646 (mp10) cc_final: 0.7400 (mp10) REVERT: C 415 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.4696 (tp30) REVERT: D 337 PHE cc_start: 0.8448 (t80) cc_final: 0.7979 (t80) outliers start: 30 outliers final: 23 residues processed: 184 average time/residue: 0.3588 time to fit residues: 103.6038 Evaluate side-chains 182 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 111 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 106 optimal weight: 0.0070 chunk 126 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.150860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117384 restraints weight = 15085.732| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.38 r_work: 0.3197 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12593 Z= 0.106 Angle : 0.491 10.602 17066 Z= 0.247 Chirality : 0.040 0.411 1919 Planarity : 0.003 0.042 2163 Dihedral : 4.453 54.344 1803 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.31 % Allowed : 15.75 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1524 helix: 1.81 (0.22), residues: 596 sheet: -1.69 (0.33), residues: 268 loop : -1.32 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 296 HIS 0.005 0.001 HIS B 328 PHE 0.027 0.001 PHE A 337 TYR 0.022 0.001 TYR A 44 ARG 0.005 0.000 ARG A 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00775 ( 7) link_NAG-ASN : angle 3.63745 ( 21) hydrogen bonds : bond 0.03086 ( 487) hydrogen bonds : angle 4.04311 ( 1395) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.37579 ( 8) covalent geometry : bond 0.00249 (12582) covalent geometry : angle 0.47470 (17037) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.6907 (t0) cc_final: 0.6670 (t0) REVERT: A 84 ASN cc_start: 0.8085 (m110) cc_final: 0.7248 (t0) REVERT: A 153 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: A 229 ASP cc_start: 0.8054 (t0) cc_final: 0.7842 (t0) REVERT: B 359 PHE cc_start: 0.7939 (t80) cc_final: 0.7586 (t80) REVERT: C 210 ASP cc_start: 0.7520 (m-30) cc_final: 0.7158 (p0) REVERT: C 241 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7416 (mt0) REVERT: C 288 GLN cc_start: 0.7573 (mp10) cc_final: 0.7330 (mp10) REVERT: C 337 PHE cc_start: 0.7916 (t80) cc_final: 0.7621 (t80) REVERT: C 415 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.4660 (tp30) REVERT: D 337 PHE cc_start: 0.8396 (t80) cc_final: 0.7537 (t80) REVERT: D 360 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8339 (tpt) outliers start: 31 outliers final: 25 residues processed: 181 average time/residue: 0.3234 time to fit residues: 89.5602 Evaluate side-chains 184 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 112 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115946 restraints weight = 15255.339| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.45 r_work: 0.3159 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12593 Z= 0.146 Angle : 0.518 11.235 17066 Z= 0.259 Chirality : 0.041 0.416 1919 Planarity : 0.003 0.042 2163 Dihedral : 4.494 54.661 1803 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.16 % Allowed : 16.04 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1524 helix: 1.74 (0.22), residues: 596 sheet: -1.73 (0.33), residues: 268 loop : -1.37 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.005 0.001 HIS B 328 PHE 0.029 0.001 PHE A 337 TYR 0.022 0.002 TYR A 44 ARG 0.002 0.000 ARG C 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 7) link_NAG-ASN : angle 3.63343 ( 21) hydrogen bonds : bond 0.03288 ( 487) hydrogen bonds : angle 4.07501 ( 1395) SS BOND : bond 0.00121 ( 4) SS BOND : angle 0.42006 ( 8) covalent geometry : bond 0.00353 (12582) covalent geometry : angle 0.50201 (17037) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7826 (mp) cc_final: 0.7143 (pt) REVERT: A 79 ASP cc_start: 0.6735 (t0) cc_final: 0.6480 (t0) REVERT: A 84 ASN cc_start: 0.8307 (m110) cc_final: 0.7451 (t0) REVERT: A 153 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: A 196 ASN cc_start: 0.7470 (p0) cc_final: 0.7155 (p0) REVERT: A 229 ASP cc_start: 0.8119 (t0) cc_final: 0.7897 (t0) REVERT: B 359 PHE cc_start: 0.8058 (t80) cc_final: 0.7737 (t80) REVERT: C 210 ASP cc_start: 0.7572 (m-30) cc_final: 0.7178 (p0) REVERT: C 241 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7480 (mt0) REVERT: C 288 GLN cc_start: 0.7635 (mp10) cc_final: 0.7394 (mp10) REVERT: C 337 PHE cc_start: 0.7987 (t80) cc_final: 0.7727 (t80) REVERT: C 415 GLU cc_start: 0.6275 (OUTLIER) cc_final: 0.4732 (tp30) REVERT: D 360 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8668 (tpt) outliers start: 29 outliers final: 25 residues processed: 179 average time/residue: 0.2069 time to fit residues: 56.0763 Evaluate side-chains 184 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 100 optimal weight: 0.0570 chunk 78 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 126 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 141 optimal weight: 0.0170 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 HIS C 348 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.153881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118374 restraints weight = 15112.629| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.59 r_work: 0.3231 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12593 Z= 0.100 Angle : 0.479 10.452 17066 Z= 0.241 Chirality : 0.040 0.404 1919 Planarity : 0.003 0.042 2163 Dihedral : 4.334 54.211 1803 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.24 % Allowed : 15.82 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1524 helix: 1.88 (0.22), residues: 592 sheet: -1.65 (0.33), residues: 268 loop : -1.23 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.005 0.001 HIS B 328 PHE 0.026 0.001 PHE A 337 TYR 0.022 0.001 TYR A 44 ARG 0.002 0.000 ARG A 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00712 ( 7) link_NAG-ASN : angle 3.45716 ( 21) hydrogen bonds : bond 0.02994 ( 487) hydrogen bonds : angle 4.00974 ( 1395) SS BOND : bond 0.00090 ( 4) SS BOND : angle 0.31591 ( 8) covalent geometry : bond 0.00232 (12582) covalent geometry : angle 0.46326 (17037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5995.41 seconds wall clock time: 109 minutes 19.47 seconds (6559.47 seconds total)