Starting phenix.real_space_refine on Sat Aug 23 13:03:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5y_45237/08_2025/9c5y_45237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5y_45237/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9c5y_45237/08_2025/9c5y_45237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5y_45237/08_2025/9c5y_45237.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c5y_45237/08_2025/9c5y_45237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5y_45237/08_2025/9c5y_45237.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.22, per 1000 atoms: 0.26 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: 0.87 Conformation dependent library (CDL) restraints added in 618.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.34 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: 1.85 Time building geometry restraints manager: 1.22 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 1001) selection = (chain 'B' and resid 33 through 1001) selection = chain 'C' selection = (chain 'D' and resid 33 through 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.120 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- 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 : 9.07 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG A 270 TYR 0.018 0.001 TYR C 252 PHE 0.017 0.001 PHE A 337 TRP 0.011 0.001 TRP B 296 HIS 0.003 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00332 (12582) covalent geometry : angle 0.51974 (17037) SS BOND : bond 0.00145 ( 4) SS BOND : angle 0.48094 ( 8) hydrogen bonds : bond 0.12862 ( 487) hydrogen bonds : angle 5.61834 ( 1395) link_NAG-ASN : bond 0.00614 ( 7) link_NAG-ASN : angle 3.68272 ( 21) *********************** 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 : 0.477 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: 0.1102 time to fit residues: 31.6892 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 : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.152092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117510 restraints weight = 15254.595| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.48 r_work: 0.3198 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12593 Z= 0.148 Angle : 0.524 11.003 17066 Z= 0.266 Chirality : 0.042 0.477 1919 Planarity : 0.004 0.047 2163 Dihedral : 5.155 54.947 1803 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.82 % Allowed : 7.61 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.22), residues: 1524 helix: 1.66 (0.22), residues: 588 sheet: -2.17 (0.38), residues: 188 loop : -1.39 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 270 TYR 0.025 0.001 TYR C 324 PHE 0.038 0.001 PHE A 337 TRP 0.010 0.001 TRP B 296 HIS 0.006 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00355 (12582) covalent geometry : angle 0.50830 (17037) SS BOND : bond 0.00113 ( 4) SS BOND : angle 0.36029 ( 8) hydrogen bonds : bond 0.03710 ( 487) hydrogen bonds : angle 4.40201 ( 1395) link_NAG-ASN : bond 0.00781 ( 7) link_NAG-ASN : angle 3.64705 ( 21) *********************** 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 186 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7668 (mp) cc_final: 0.7031 (pt) REVERT: A 79 ASP cc_start: 0.6864 (t0) cc_final: 0.6566 (t0) REVERT: A 140 ASP cc_start: 0.7438 (t70) cc_final: 0.7216 (t0) REVERT: A 229 ASP cc_start: 0.8191 (t0) cc_final: 0.7977 (t0) REVERT: A 340 MET cc_start: 0.6590 (mtp) cc_final: 0.6086 (ttm) REVERT: B 64 ILE cc_start: 0.8618 (mp) cc_final: 0.8403 (mp) REVERT: B 412 ASN cc_start: 0.8779 (t0) cc_final: 0.8500 (t0) REVERT: C 55 LEU cc_start: 0.7297 (mt) cc_final: 0.7009 (mt) REVERT: C 337 PHE cc_start: 0.7709 (t80) cc_final: 0.7447 (t80) outliers start: 11 outliers final: 7 residues processed: 180 average time/residue: 0.0803 time to fit residues: 21.6285 Evaluate side-chains 169 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 162 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain C residue 138 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 121 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.149224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113236 restraints weight = 15475.974| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.55 r_work: 0.3136 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1258 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= 0.219 Angle : 0.554 11.584 17066 Z= 0.281 Chirality : 0.043 0.448 1919 Planarity : 0.004 0.047 2163 Dihedral : 5.158 59.426 1803 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.09 % Allowed : 11.04 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.22), residues: 1524 helix: 1.48 (0.22), residues: 588 sheet: -2.02 (0.35), residues: 228 loop : -1.54 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 270 TYR 0.019 0.002 TYR D 44 PHE 0.036 0.001 PHE A 337 TRP 0.011 0.001 TRP B 296 HIS 0.003 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00529 (12582) covalent geometry : angle 0.53860 (17037) SS BOND : bond 0.00207 ( 4) SS BOND : angle 0.59335 ( 8) hydrogen bonds : bond 0.03803 ( 487) hydrogen bonds : angle 4.29635 ( 1395) link_NAG-ASN : bond 0.00583 ( 7) link_NAG-ASN : angle 3.75633 ( 21) *********************** 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 200 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7756 (mp) cc_final: 0.7092 (pt) REVERT: A 79 ASP cc_start: 0.6899 (t0) cc_final: 0.6496 (t0) REVERT: A 84 ASN cc_start: 0.8116 (m110) cc_final: 0.7171 (t0) REVERT: A 229 ASP cc_start: 0.8242 (t0) cc_final: 0.7992 (t0) REVERT: B 64 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8456 (mp) REVERT: B 156 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7816 (mt) REVERT: B 412 ASN cc_start: 0.8776 (t0) cc_final: 0.8557 (t0) REVERT: C 55 LEU cc_start: 0.7317 (mt) cc_final: 0.7038 (mt) REVERT: C 210 ASP cc_start: 0.7584 (m-30) cc_final: 0.7285 (p0) REVERT: C 288 GLN cc_start: 0.7627 (mp10) cc_final: 0.7378 (mp10) REVERT: C 337 PHE cc_start: 0.7903 (t80) cc_final: 0.7681 (t80) REVERT: C 379 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8282 (tptp) REVERT: D 68 ARG cc_start: 0.7799 (mmp80) cc_final: 0.7452 (mmp80) outliers start: 28 outliers final: 17 residues processed: 184 average time/residue: 0.1001 time to fit residues: 27.3989 Evaluate side-chains 183 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 64 ILE Chi-restraints excluded: chain B residue 156 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 138 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 247 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 106 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 130 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.151320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117922 restraints weight = 15165.906| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.36 r_work: 0.3218 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12593 Z= 0.105 Angle : 0.475 10.829 17066 Z= 0.241 Chirality : 0.040 0.425 1919 Planarity : 0.003 0.045 2163 Dihedral : 4.792 54.206 1803 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.64 % Allowed : 12.99 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.22), residues: 1524 helix: 1.78 (0.22), residues: 588 sheet: -1.74 (0.33), residues: 268 loop : -1.45 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 270 TYR 0.019 0.001 TYR D 44 PHE 0.027 0.001 PHE A 337 TRP 0.008 0.001 TRP B 296 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00246 (12582) covalent geometry : angle 0.45961 (17037) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.38570 ( 8) hydrogen bonds : bond 0.03143 ( 487) hydrogen bonds : angle 4.09934 ( 1395) link_NAG-ASN : bond 0.00710 ( 7) link_NAG-ASN : angle 3.50433 ( 21) *********************** 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 199 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7704 (mp) cc_final: 0.7019 (pt) REVERT: A 79 ASP cc_start: 0.7038 (t0) cc_final: 0.6685 (t0) REVERT: A 229 ASP cc_start: 0.8304 (t0) cc_final: 0.8100 (t0) REVERT: C 55 LEU cc_start: 0.7461 (mt) cc_final: 0.7113 (mt) REVERT: C 210 ASP cc_start: 0.7605 (m-30) cc_final: 0.7119 (p0) REVERT: C 288 GLN cc_start: 0.7520 (mp10) cc_final: 0.7300 (mp10) outliers start: 22 outliers final: 13 residues processed: 189 average time/residue: 0.1080 time to fit residues: 29.8718 Evaluate side-chains 174 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain C residue 77 THR 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 332 VAL Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 0.8980 chunk 86 optimal weight: 0.0070 chunk 89 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 99 optimal weight: 0.0970 chunk 76 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.150792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116102 restraints weight = 15326.320| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.48 r_work: 0.3173 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1399 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= 0.144 Angle : 0.501 11.037 17066 Z= 0.253 Chirality : 0.041 0.424 1919 Planarity : 0.004 0.045 2163 Dihedral : 4.713 53.905 1803 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.16 % Allowed : 13.58 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.22), residues: 1524 helix: 1.74 (0.22), residues: 588 sheet: -1.71 (0.33), residues: 268 loop : -1.47 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 133 TYR 0.019 0.001 TYR D 44 PHE 0.025 0.001 PHE A 337 TRP 0.010 0.001 TRP B 296 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00347 (12582) covalent geometry : angle 0.48532 (17037) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.44188 ( 8) hydrogen bonds : bond 0.03289 ( 487) hydrogen bonds : angle 4.06801 ( 1395) link_NAG-ASN : bond 0.00640 ( 7) link_NAG-ASN : angle 3.52733 ( 21) *********************** 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 194 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7748 (mp) cc_final: 0.7046 (pt) REVERT: A 79 ASP cc_start: 0.6840 (t0) cc_final: 0.6467 (t0) REVERT: A 84 ASN cc_start: 0.8327 (m110) cc_final: 0.7405 (t0) REVERT: A 229 ASP cc_start: 0.8175 (t0) cc_final: 0.7964 (t0) REVERT: B 64 ILE cc_start: 0.8582 (mp) cc_final: 0.8287 (mp) REVERT: B 156 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7847 (mt) REVERT: C 149 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8432 (mp) REVERT: C 210 ASP cc_start: 0.7582 (m-30) cc_final: 0.7166 (p0) REVERT: C 288 GLN cc_start: 0.7592 (mp10) cc_final: 0.7348 (mp10) REVERT: C 415 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.4831 (tp30) REVERT: D 337 PHE cc_start: 0.8381 (t80) cc_final: 0.7726 (t80) outliers start: 29 outliers final: 22 residues processed: 183 average time/residue: 0.0931 time to fit residues: 25.4915 Evaluate side-chains 183 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 367 HIS 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 57 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 0.0470 chunk 74 optimal weight: 0.9990 chunk 121 optimal weight: 0.0970 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 D 136 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118690 restraints weight = 15157.551| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.42 r_work: 0.3224 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1492 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= 0.098 Angle : 0.462 10.804 17066 Z= 0.233 Chirality : 0.040 0.415 1919 Planarity : 0.003 0.044 2163 Dihedral : 4.416 53.827 1803 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.61 % Allowed : 13.96 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.23), residues: 1524 helix: 1.94 (0.22), residues: 588 sheet: -1.64 (0.33), residues: 276 loop : -1.35 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 270 TYR 0.020 0.001 TYR D 44 PHE 0.019 0.001 PHE A 337 TRP 0.009 0.001 TRP B 296 HIS 0.003 0.001 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00227 (12582) covalent geometry : angle 0.44665 (17037) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.32441 ( 8) hydrogen bonds : bond 0.02963 ( 487) hydrogen bonds : angle 3.98422 ( 1395) link_NAG-ASN : bond 0.00716 ( 7) link_NAG-ASN : angle 3.43063 ( 21) *********************** 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 210 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7823 (mp) cc_final: 0.7288 (pt) REVERT: A 79 ASP cc_start: 0.6845 (t0) cc_final: 0.6461 (t0) REVERT: A 84 ASN cc_start: 0.8211 (m110) cc_final: 0.7331 (t0) REVERT: A 153 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: C 44 TYR cc_start: 0.7821 (t80) cc_final: 0.7491 (t80) REVERT: C 210 ASP cc_start: 0.7527 (m-30) cc_final: 0.7118 (p0) REVERT: C 288 GLN cc_start: 0.7524 (mp10) cc_final: 0.7285 (mp10) REVERT: C 337 PHE cc_start: 0.7866 (t80) cc_final: 0.7602 (t80) REVERT: D 337 PHE cc_start: 0.8387 (t80) cc_final: 0.8070 (t80) outliers start: 35 outliers final: 23 residues processed: 198 average time/residue: 0.0985 time to fit residues: 29.3783 Evaluate side-chains 188 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 245 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 78 TYR 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 332 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 367 HIS 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 26 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.149825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116445 restraints weight = 15160.097| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.36 r_work: 0.3181 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1551 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= 0.135 Angle : 0.491 11.121 17066 Z= 0.246 Chirality : 0.041 0.418 1919 Planarity : 0.003 0.044 2163 Dihedral : 4.397 54.020 1803 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.09 % Allowed : 15.00 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.22), residues: 1524 helix: 1.87 (0.22), residues: 596 sheet: -1.67 (0.33), residues: 268 loop : -1.36 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 68 TYR 0.020 0.001 TYR D 44 PHE 0.023 0.001 PHE A 337 TRP 0.009 0.001 TRP B 296 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00324 (12582) covalent geometry : angle 0.47570 (17037) SS BOND : bond 0.00149 ( 4) SS BOND : angle 0.42397 ( 8) hydrogen bonds : bond 0.03236 ( 487) hydrogen bonds : angle 3.99229 ( 1395) link_NAG-ASN : bond 0.00639 ( 7) link_NAG-ASN : angle 3.47836 ( 21) *********************** 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 194 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7857 (mp) cc_final: 0.7282 (pt) REVERT: A 79 ASP cc_start: 0.6866 (t0) cc_final: 0.6491 (t0) REVERT: A 84 ASN cc_start: 0.8256 (m110) cc_final: 0.7470 (t0) REVERT: A 153 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: B 359 PHE cc_start: 0.8134 (t80) cc_final: 0.7873 (t80) REVERT: C 210 ASP cc_start: 0.7544 (m-30) cc_final: 0.7177 (p0) REVERT: C 241 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7375 (mt0) REVERT: C 248 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7779 (mmt) REVERT: C 288 GLN cc_start: 0.7580 (mp10) cc_final: 0.7338 (mp10) REVERT: C 337 PHE cc_start: 0.7789 (t80) cc_final: 0.7556 (t80) REVERT: C 379 LYS cc_start: 0.8350 (mmmt) cc_final: 0.8128 (tptp) REVERT: C 415 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.4800 (tp30) REVERT: D 337 PHE cc_start: 0.8517 (t80) cc_final: 0.8025 (t80) outliers start: 28 outliers final: 22 residues processed: 184 average time/residue: 0.1006 time to fit residues: 27.9534 Evaluate side-chains 187 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 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 241 GLN Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 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 332 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 367 HIS 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 34 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.150287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115709 restraints weight = 15294.272| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.44 r_work: 0.3163 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1599 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= 0.150 Angle : 0.508 11.255 17066 Z= 0.256 Chirality : 0.041 0.421 1919 Planarity : 0.003 0.044 2163 Dihedral : 4.461 54.303 1803 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.24 % Allowed : 15.67 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.22), residues: 1524 helix: 1.80 (0.22), residues: 596 sheet: -1.72 (0.33), residues: 268 loop : -1.37 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 68 TYR 0.019 0.001 TYR D 44 PHE 0.023 0.001 PHE A 337 TRP 0.009 0.001 TRP B 296 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00362 (12582) covalent geometry : angle 0.49310 (17037) SS BOND : bond 0.00161 ( 4) SS BOND : angle 0.46368 ( 8) hydrogen bonds : bond 0.03303 ( 487) hydrogen bonds : angle 4.01851 ( 1395) link_NAG-ASN : bond 0.00624 ( 7) link_NAG-ASN : angle 3.53531 ( 21) *********************** 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 193 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7867 (mp) cc_final: 0.7264 (pt) REVERT: A 79 ASP cc_start: 0.6834 (t0) cc_final: 0.6451 (t0) REVERT: A 84 ASN cc_start: 0.8326 (m110) cc_final: 0.7458 (t0) REVERT: A 153 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7277 (m-80) REVERT: B 359 PHE cc_start: 0.8089 (t80) cc_final: 0.7690 (t80) REVERT: C 210 ASP cc_start: 0.7566 (m-30) cc_final: 0.7191 (p0) REVERT: C 241 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7398 (mt0) REVERT: C 248 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7869 (mmp) REVERT: C 288 GLN cc_start: 0.7645 (mp10) cc_final: 0.7395 (mp10) REVERT: C 379 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8186 (tptp) REVERT: C 415 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.4754 (tp30) REVERT: D 337 PHE cc_start: 0.8449 (t80) cc_final: 0.7981 (t80) outliers start: 30 outliers final: 23 residues processed: 181 average time/residue: 0.0893 time to fit residues: 24.4784 Evaluate side-chains 181 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 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 241 GLN Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 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 332 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 380 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.150760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116836 restraints weight = 15183.765| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.41 r_work: 0.3190 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12593 Z= 0.118 Angle : 0.492 10.838 17066 Z= 0.246 Chirality : 0.041 0.411 1919 Planarity : 0.003 0.043 2163 Dihedral : 4.393 54.203 1803 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.31 % Allowed : 15.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.22), residues: 1524 helix: 1.84 (0.22), residues: 596 sheet: -1.69 (0.33), residues: 268 loop : -1.34 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 354 TYR 0.016 0.001 TYR B 44 PHE 0.023 0.001 PHE A 337 TRP 0.008 0.001 TRP B 296 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00279 (12582) covalent geometry : angle 0.47710 (17037) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.39093 ( 8) hydrogen bonds : bond 0.03131 ( 487) hydrogen bonds : angle 3.99474 ( 1395) link_NAG-ASN : bond 0.00675 ( 7) link_NAG-ASN : angle 3.46455 ( 21) *********************** 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 190 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7862 (mp) cc_final: 0.7249 (pt) REVERT: A 79 ASP cc_start: 0.6810 (t0) cc_final: 0.6433 (t0) REVERT: A 84 ASN cc_start: 0.8274 (m110) cc_final: 0.7428 (t0) REVERT: A 153 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7264 (m-80) REVERT: A 229 ASP cc_start: 0.8109 (t0) cc_final: 0.7832 (t0) REVERT: B 359 PHE cc_start: 0.8003 (t80) cc_final: 0.7607 (t80) REVERT: C 210 ASP cc_start: 0.7521 (m-30) cc_final: 0.7153 (p0) REVERT: C 241 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7387 (mt0) REVERT: C 248 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7793 (mmp) REVERT: C 288 GLN cc_start: 0.7581 (mp10) cc_final: 0.7331 (mp10) REVERT: C 337 PHE cc_start: 0.7890 (t80) cc_final: 0.7536 (t80) REVERT: C 415 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.4683 (tp30) REVERT: D 337 PHE cc_start: 0.8319 (t80) cc_final: 0.7802 (t80) outliers start: 31 outliers final: 25 residues processed: 178 average time/residue: 0.0826 time to fit residues: 22.4145 Evaluate side-chains 188 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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 241 GLN Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 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 332 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 367 HIS 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 135 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.150670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116782 restraints weight = 15246.262| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.40 r_work: 0.3189 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12593 Z= 0.125 Angle : 0.497 10.919 17066 Z= 0.248 Chirality : 0.041 0.412 1919 Planarity : 0.003 0.043 2163 Dihedral : 4.389 54.284 1803 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.16 % Allowed : 16.27 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.22), residues: 1524 helix: 1.83 (0.22), residues: 596 sheet: -1.70 (0.33), residues: 268 loop : -1.33 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 354 TYR 0.016 0.001 TYR B 252 PHE 0.024 0.001 PHE A 337 TRP 0.009 0.001 TRP B 296 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00298 (12582) covalent geometry : angle 0.48162 (17037) SS BOND : bond 0.00140 ( 4) SS BOND : angle 0.40442 ( 8) hydrogen bonds : bond 0.03157 ( 487) hydrogen bonds : angle 3.98643 ( 1395) link_NAG-ASN : bond 0.00658 ( 7) link_NAG-ASN : angle 3.48295 ( 21) ********************** 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 185 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7829 (mp) cc_final: 0.7266 (pt) REVERT: A 79 ASP cc_start: 0.6819 (t0) cc_final: 0.6443 (t0) REVERT: A 84 ASN cc_start: 0.8304 (m110) cc_final: 0.7450 (t0) REVERT: A 153 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: A 229 ASP cc_start: 0.8098 (t0) cc_final: 0.7816 (t0) REVERT: B 359 PHE cc_start: 0.8005 (t80) cc_final: 0.7656 (t80) REVERT: C 210 ASP cc_start: 0.7510 (m-30) cc_final: 0.7153 (p0) REVERT: C 241 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7405 (mt0) REVERT: C 288 GLN cc_start: 0.7592 (mp10) cc_final: 0.7341 (mp10) REVERT: C 337 PHE cc_start: 0.7915 (t80) cc_final: 0.7606 (t80) REVERT: C 415 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.4574 (tp30) REVERT: D 337 PHE cc_start: 0.8240 (t80) cc_final: 0.7971 (t80) outliers start: 29 outliers final: 25 residues processed: 173 average time/residue: 0.0858 time to fit residues: 23.2352 Evaluate side-chains 180 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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 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 367 HIS Chi-restraints excluded: chain D residue 380 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 109 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 18 optimal weight: 0.0010 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117495 restraints weight = 15236.814| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.42 r_work: 0.3197 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12593 Z= 0.112 Angle : 0.497 10.752 17066 Z= 0.247 Chirality : 0.041 0.409 1919 Planarity : 0.003 0.043 2163 Dihedral : 4.374 54.210 1803 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.31 % Allowed : 16.19 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.22), residues: 1524 helix: 1.89 (0.22), residues: 592 sheet: -1.67 (0.33), residues: 268 loop : -1.26 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 354 TYR 0.016 0.001 TYR B 44 PHE 0.023 0.001 PHE A 337 TRP 0.009 0.001 TRP B 296 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00264 (12582) covalent geometry : angle 0.48259 (17037) SS BOND : bond 0.00131 ( 4) SS BOND : angle 0.34182 ( 8) hydrogen bonds : bond 0.03072 ( 487) hydrogen bonds : angle 4.01053 ( 1395) link_NAG-ASN : bond 0.00695 ( 7) link_NAG-ASN : angle 3.44485 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2510.27 seconds wall clock time: 43 minutes 59.79 seconds (2639.79 seconds total)