Starting phenix.real_space_refine on Thu Jul 2 20:57:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tyn_26188/07_2026/7tyn_26188.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyn_26188/07_2026/7tyn_26188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyn_26188/07_2026/7tyn_26188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyn_26188/07_2026/7tyn_26188.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyn_26188/07_2026/7tyn_26188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyn_26188/07_2026/7tyn_26188.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tyn_26188/07_2026/7tyn_26188.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tyn_26188/07_2026/7tyn_26188.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 543 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 63 5.16 5 C 6025 2.51 5 N 1581 2.21 5 O 1694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9364 Number of models: 1 Model: "" Number of chains: 8 Chain: "P" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2892 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 17, 'TRANS': 355} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 8, 'GLN:plan1': 4, 'TYR:plan': 5, 'GLU:plan': 4, 'TRP:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 132 Chain: "A" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1881 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Unusual residues: {'NAG': 2, 'P42': 1, 'PLM': 13, 'Y01': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.86, per 1000 atoms: 0.20 Number of scatterers: 9364 At special positions: 0 Unit cell: (94.1673, 158.153, 90.5455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 1 15.00 O 1694 8.00 N 1581 7.00 C 6025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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=1, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " " NAG R 502 " - " ASN R 73 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 240.8 milliseconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 13 sheets defined 41.8% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 21 Processing helix chain 'R' and resid 38 through 62 removed outlier: 3.703A pdb=" N TYR R 56 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 137 removed outlier: 3.867A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE R 137 " --> pdb=" O MET R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.504A pdb=" N VAL R 205 " --> pdb=" O HIS R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.555A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 4.247A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.652A pdb=" N TRP R 290 " --> pdb=" O ASP R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 329 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 348 Processing helix chain 'R' and resid 348 through 353 Processing helix chain 'R' and resid 354 through 359 removed outlier: 3.539A pdb=" N PHE R 359 " --> pdb=" O GLN R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 409 removed outlier: 3.854A pdb=" N THR R 401 " --> pdb=" O GLU R 397 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE R 409 " --> pdb=" O GLN R 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.500A pdb=" N ARG A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.635A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.677A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.575A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.650A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.757A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.668A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.530A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.686A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA2, first strand: chain 'R' and resid 89 through 94 removed outlier: 3.922A pdb=" N VAL R 89 " --> pdb=" O CYS R 112 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS R 112 " --> pdb=" O VAL R 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.967A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.274A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.867A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.682A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.573A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.784A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.498A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.696A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.844A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1311 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: 1.53 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1550 1.32 - 1.45: 2578 1.45 - 1.57: 5340 1.57 - 1.70: 2 1.70 - 1.82: 88 Bond restraints: 9558 Sorted by residual: bond pdb=" C1 NAG R 502 " pdb=" O5 NAG R 502 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.23e+01 bond pdb=" N GLY P 28 " pdb=" CA GLY P 28 " ideal model delta sigma weight residual 1.447 1.476 -0.029 9.40e-03 1.13e+04 9.31e+00 bond pdb=" N LEU R 80 " pdb=" CA LEU R 80 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.51e+00 bond pdb=" OBN P42 R 503 " pdb=" PBM P42 R 503 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.51e+00 ... (remaining 9553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.52: 12871 4.52 - 9.03: 12 9.03 - 13.55: 0 13.55 - 18.06: 0 18.06 - 22.58: 2 Bond angle restraints: 12885 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 90.04 21.96 1.40e+00 5.10e-01 2.46e+02 angle pdb=" C THR P 31 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 125.00 147.58 -22.58 4.10e+00 5.95e-02 3.03e+01 angle pdb=" C THR P 27 " pdb=" CA THR P 27 " pdb=" CB THR P 27 " ideal model delta sigma weight residual 111.80 119.64 -7.84 1.46e+00 4.69e-01 2.88e+01 angle pdb=" N GLY R 78 " pdb=" CA GLY R 78 " pdb=" C GLY R 78 " ideal model delta sigma weight residual 114.37 108.36 6.01 1.26e+00 6.30e-01 2.27e+01 angle pdb=" N TYR R 131 " pdb=" CA TYR R 131 " pdb=" C TYR R 131 " ideal model delta sigma weight residual 112.92 107.38 5.54 1.23e+00 6.61e-01 2.03e+01 ... (remaining 12880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 5234 17.48 - 34.97: 354 34.97 - 52.45: 75 52.45 - 69.93: 21 69.93 - 87.41: 11 Dihedral angle restraints: 5695 sinusoidal: 2336 harmonic: 3359 Sorted by residual: dihedral pdb=" CB CYS R 72 " pdb=" SG CYS R 72 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual -86.00 -27.30 -58.70 1 1.00e+01 1.00e-02 4.61e+01 dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 40.92 52.08 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -149.92 -30.08 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 5692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1400 0.120 - 0.239: 9 0.239 - 0.359: 3 0.359 - 0.479: 0 0.479 - 0.599: 1 Chirality restraints: 1413 Sorted by residual: chirality pdb=" C1 NAG R 501 " pdb=" ND2 ASN R 130 " pdb=" C2 NAG R 501 " pdb=" O5 NAG R 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.96e+00 chirality pdb=" CA THR P 27 " pdb=" N THR P 27 " pdb=" C THR P 27 " pdb=" CB THR P 27 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA TRP R 76 " pdb=" N TRP R 76 " pdb=" C TRP R 76 " pdb=" CB TRP R 76 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1410 not shown) Planarity restraints: 1622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR P 31 " -0.049 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO P 32 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO R 304 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B 236 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.018 5.00e-02 4.00e+02 ... (remaining 1619 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1097 2.75 - 3.29: 8785 3.29 - 3.83: 15304 3.83 - 4.36: 19777 4.36 - 4.90: 32888 Nonbonded interactions: 77851 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.216 3.040 nonbonded pdb=" O TYR R 374 " pdb=" OG SER R 378 " model vdw 2.256 3.040 nonbonded pdb=" OD2 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.262 3.040 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.264 3.120 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.279 3.040 ... (remaining 77846 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.580 Find NCS groups from input model: 0.040 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:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.004 0.108 9568 Z= 0.242 Angle : 0.629 22.577 12905 Z= 0.364 Chirality : 0.045 0.599 1413 Planarity : 0.003 0.064 1620 Dihedral : 13.170 87.415 3504 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.01 % Allowed : 12.88 % Favored : 85.11 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.21), residues: 1138 helix: -3.02 (0.16), residues: 414 sheet: -0.75 (0.30), residues: 253 loop : -1.29 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 118 TYR 0.010 0.001 TYR R 98 PHE 0.012 0.001 PHE N 108 TRP 0.012 0.001 TRP R 76 HIS 0.005 0.001 HIS R 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.22 ( 9558) covalent geometry : angle 0.62292 / 0.36 (12885) SS BOND : bond 0.00177 / 0.12 ( 7) SS BOND : angle 1.57224 / 1.38 ( 14) hydrogen bonds : bond 0.25416 / 17.59 ( 459) hydrogen bonds : angle 8.82907 / 6.32 ( 1311) Misc. bond : bond 0.10849 / 5.71 ( 1) link_NAG-ASN : bond 0.00740 / 0.37 ( 2) link_NAG-ASN : angle 3.35769 / 1.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.316 Fit side-chains REVERT: P 32 PRO cc_start: 0.4510 (OUTLIER) cc_final: 0.4118 (Cg_exo) REVERT: R 143 LYS cc_start: 0.7422 (ttmt) cc_final: 0.7103 (ttmt) REVERT: R 174 ARG cc_start: 0.7704 (mmm-85) cc_final: 0.7389 (mtm-85) REVERT: R 229 MET cc_start: 0.8624 (tpp) cc_final: 0.8364 (tpp) REVERT: R 230 MET cc_start: 0.8015 (ttm) cc_final: 0.7812 (ttm) REVERT: R 337 MET cc_start: 0.7876 (ttp) cc_final: 0.7427 (ttm) REVERT: A 53 LYS cc_start: 0.7514 (ttpt) cc_final: 0.6783 (tttt) REVERT: A 221 MET cc_start: 0.8337 (ttp) cc_final: 0.7996 (ttp) REVERT: A 356 ARG cc_start: 0.7042 (mtm180) cc_final: 0.6839 (ptt180) REVERT: A 358 TYR cc_start: 0.8075 (m-80) cc_final: 0.7782 (m-80) REVERT: B 9 GLN cc_start: 0.7469 (tt0) cc_final: 0.7230 (tm-30) REVERT: B 19 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7710 (ttp80) REVERT: B 266 HIS cc_start: 0.7880 (t-170) cc_final: 0.7576 (t70) REVERT: G 14 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7518 (ptpt) REVERT: G 38 MET cc_start: 0.8421 (ttp) cc_final: 0.8092 (ttm) REVERT: N 19 ARG cc_start: 0.8694 (ttt90) cc_final: 0.8397 (ttt180) REVERT: N 46 GLU cc_start: 0.7742 (tt0) cc_final: 0.7448 (tt0) REVERT: N 50 ASP cc_start: 0.8635 (p0) cc_final: 0.8406 (p0) REVERT: N 123 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8554 (mm-40) outliers start: 19 outliers final: 5 residues processed: 204 average time/residue: 0.5813 time to fit residues: 125.5510 Evaluate side-chains 154 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 32 PRO Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain N residue 12 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 50.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 135 ASN R 179 GLN R 227 GLN R 302 HIS R 383 GLN A 35 GLN B 132 ASN B 220 GLN G 24 ASN ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.170431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121381 restraints weight = 9597.679| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.02 r_work: 0.3078 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9568 Z= 0.145 Angle : 0.568 8.042 12905 Z= 0.297 Chirality : 0.043 0.273 1413 Planarity : 0.004 0.045 1620 Dihedral : 6.503 69.968 1489 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.59 % Allowed : 16.68 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.23), residues: 1138 helix: -0.09 (0.23), residues: 437 sheet: -0.35 (0.32), residues: 234 loop : -0.83 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 72 TYR 0.012 0.001 TYR R 391 PHE 0.016 0.002 PHE R 172 TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 9558) covalent geometry : angle 0.56439 / 0.30 (12885) SS BOND : bond 0.00458 / 0.26 ( 7) SS BOND : angle 2.03208 / 1.67 ( 14) hydrogen bonds : bond 0.04971 / 3.39 ( 459) hydrogen bonds : angle 4.99563 / 3.57 ( 1311) Misc. bond : bond 0.00044 / 0.02 ( 1) link_NAG-ASN : bond 0.00886 / 0.46 ( 2) link_NAG-ASN : angle 0.99847 / 0.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.350 Fit side-chains REVERT: R 112 CYS cc_start: -0.0685 (OUTLIER) cc_final: -0.0981 (m) REVERT: R 140 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6907 (tp30) REVERT: R 174 ARG cc_start: 0.7540 (mmm-85) cc_final: 0.7251 (mtm-85) REVERT: R 204 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6368 (mm-30) REVERT: R 229 MET cc_start: 0.8747 (tpp) cc_final: 0.8434 (mmm) REVERT: R 337 MET cc_start: 0.7669 (ttp) cc_final: 0.7345 (ttm) REVERT: R 405 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7102 (tm-30) REVERT: A 221 MET cc_start: 0.9037 (ttp) cc_final: 0.8803 (ttp) REVERT: A 358 TYR cc_start: 0.8557 (m-80) cc_final: 0.8181 (m-80) REVERT: B 19 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7268 (ttp80) REVERT: B 61 MET cc_start: 0.8920 (ppp) cc_final: 0.8662 (ppp) REVERT: G 14 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7082 (ttmt) REVERT: G 38 MET cc_start: 0.8521 (ttp) cc_final: 0.8146 (ttm) REVERT: N 30 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8637 (p) REVERT: N 46 GLU cc_start: 0.8491 (tt0) cc_final: 0.8179 (tt0) REVERT: N 89 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8085 (pt0) outliers start: 34 outliers final: 12 residues processed: 180 average time/residue: 0.5636 time to fit residues: 107.7648 Evaluate side-chains 162 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 120 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 5 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 ASN R 227 GLN R 377 HIS R 408 GLN A 19 GLN A 31 GLN A 294 GLN B 17 GLN N 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.167772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117027 restraints weight = 9507.959| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.00 r_work: 0.3087 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9568 Z= 0.186 Angle : 0.596 8.926 12905 Z= 0.311 Chirality : 0.045 0.230 1413 Planarity : 0.004 0.039 1620 Dihedral : 7.359 67.663 1481 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.80 % Allowed : 17.11 % Favored : 79.09 % 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 are not related in a simple way. whole: -0.06 (0.23), residues: 1138 helix: 0.84 (0.24), residues: 446 sheet: -0.19 (0.32), residues: 234 loop : -0.72 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 105 TYR 0.013 0.002 TYR R 149 PHE 0.015 0.002 PHE A 212 TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 9558) covalent geometry : angle 0.58976 / 0.31 (12885) SS BOND : bond 0.00308 / 0.13 ( 7) SS BOND : angle 2.59878 / 2.19 ( 14) hydrogen bonds : bond 0.05092 / 3.48 ( 459) hydrogen bonds : angle 4.86076 / 3.48 ( 1311) Misc. bond : bond 0.00003 / 0.00 ( 1) link_NAG-ASN : bond 0.00604 / 0.32 ( 2) link_NAG-ASN : angle 0.80371 / 0.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.300 Fit side-chains REVERT: R 196 MET cc_start: 0.8479 (mtt) cc_final: 0.8222 (mtm) REVERT: R 204 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6434 (mm-30) REVERT: R 256 LYS cc_start: 0.6131 (tmtt) cc_final: 0.5887 (tptt) REVERT: R 405 GLN cc_start: 0.7612 (tm-30) cc_final: 0.7090 (tm-30) REVERT: A 221 MET cc_start: 0.9063 (ttp) cc_final: 0.8800 (ttp) REVERT: A 358 TYR cc_start: 0.8592 (m-80) cc_final: 0.8255 (m-80) REVERT: B 19 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7458 (ttp80) REVERT: B 61 MET cc_start: 0.9026 (ppp) cc_final: 0.8748 (ppp) REVERT: B 124 TYR cc_start: 0.9184 (m-80) cc_final: 0.8916 (m-80) REVERT: B 219 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8004 (mtm180) REVERT: G 38 MET cc_start: 0.8559 (ttp) cc_final: 0.8224 (ttm) REVERT: N 89 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8021 (pt0) REVERT: N 105 ARG cc_start: 0.7192 (ttp-110) cc_final: 0.6956 (mpp80) outliers start: 36 outliers final: 21 residues processed: 169 average time/residue: 0.5506 time to fit residues: 98.7151 Evaluate side-chains 161 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 120 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 ASN A 31 GLN A 213 GLN A 357 HIS B 17 GLN B 88 ASN N 1 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.166627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116748 restraints weight = 9683.685| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.09 r_work: 0.3008 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9568 Z= 0.202 Angle : 0.611 9.894 12905 Z= 0.317 Chirality : 0.046 0.193 1413 Planarity : 0.004 0.039 1620 Dihedral : 8.180 65.784 1481 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.65 % Allowed : 16.90 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1138 helix: 1.14 (0.24), residues: 446 sheet: -0.08 (0.32), residues: 234 loop : -0.59 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 98 TYR 0.014 0.002 TYR R 149 PHE 0.015 0.002 PHE A 212 TRP 0.017 0.002 TRP R 236 HIS 0.005 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 ( 9558) covalent geometry : angle 0.60363 / 0.31 (12885) SS BOND : bond 0.00462 / 0.28 ( 7) SS BOND : angle 2.75515 / 2.37 ( 14) hydrogen bonds : bond 0.04964 / 3.39 ( 459) hydrogen bonds : angle 4.77166 / 3.41 ( 1311) Misc. bond : bond 0.00006 / 0.00 ( 1) link_NAG-ASN : bond 0.00394 / 0.20 ( 2) link_NAG-ASN : angle 1.48600 / 0.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.360 Fit side-chains REVERT: R 196 MET cc_start: 0.8470 (mtt) cc_final: 0.8134 (mtp) REVERT: R 204 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6392 (mm-30) REVERT: R 256 LYS cc_start: 0.6127 (tttt) cc_final: 0.5884 (tptt) REVERT: R 280 THR cc_start: 0.8098 (m) cc_final: 0.7846 (m) REVERT: R 405 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7095 (tm-30) REVERT: A 17 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7107 (ttmm) REVERT: A 221 MET cc_start: 0.9095 (ttp) cc_final: 0.8861 (ttp) REVERT: A 356 ARG cc_start: 0.7718 (mtm110) cc_final: 0.7462 (mtm110) REVERT: A 358 TYR cc_start: 0.8614 (m-80) cc_final: 0.8266 (m-80) REVERT: B 19 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7364 (ttp80) REVERT: B 61 MET cc_start: 0.9114 (ppp) cc_final: 0.8830 (ppp) REVERT: B 124 TYR cc_start: 0.9207 (m-80) cc_final: 0.8924 (m-80) REVERT: B 219 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8120 (mtm180) REVERT: G 38 MET cc_start: 0.8577 (ttp) cc_final: 0.8191 (ttm) REVERT: N 89 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7957 (pt0) outliers start: 44 outliers final: 25 residues processed: 173 average time/residue: 0.5850 time to fit residues: 107.5008 Evaluate side-chains 166 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 120 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 11 optimal weight: 30.0000 chunk 7 optimal weight: 30.0000 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 ASN R 135 ASN R 227 GLN A 31 GLN A 292 ASN A 357 HIS B 17 GLN B 88 ASN N 1 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.168597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.119590 restraints weight = 9701.523| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.94 r_work: 0.3054 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9568 Z= 0.138 Angle : 0.548 9.529 12905 Z= 0.284 Chirality : 0.043 0.210 1413 Planarity : 0.004 0.049 1620 Dihedral : 7.685 68.149 1481 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.22 % Allowed : 17.63 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.24), residues: 1138 helix: 1.50 (0.25), residues: 447 sheet: -0.08 (0.33), residues: 234 loop : -0.45 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 105 TYR 0.013 0.001 TYR R 149 PHE 0.012 0.001 PHE B 253 TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 9558) covalent geometry : angle 0.54202 / 0.28 (12885) SS BOND : bond 0.00364 / 0.24 ( 7) SS BOND : angle 2.47058 / 2.01 ( 14) hydrogen bonds : bond 0.04279 / 2.90 ( 459) hydrogen bonds : angle 4.55460 / 3.26 ( 1311) Misc. bond : bond 0.00002 / 0.00 ( 1) link_NAG-ASN : bond 0.00469 / 0.25 ( 2) link_NAG-ASN : angle 1.23533 / 0.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.303 Fit side-chains REVERT: R 140 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6862 (tp30) REVERT: R 196 MET cc_start: 0.8442 (mtt) cc_final: 0.8101 (mtp) REVERT: R 204 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6323 (mm-30) REVERT: R 405 GLN cc_start: 0.7581 (tm-30) cc_final: 0.7076 (tm-30) REVERT: A 17 LYS cc_start: 0.7513 (ttmm) cc_final: 0.6872 (pttt) REVERT: A 19 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7781 (mt0) REVERT: A 221 MET cc_start: 0.9099 (ttp) cc_final: 0.8851 (ttp) REVERT: A 299 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6570 (tt0) REVERT: A 358 TYR cc_start: 0.8544 (m-80) cc_final: 0.8165 (m-80) REVERT: B 19 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7329 (ttp80) REVERT: B 57 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8719 (pttp) REVERT: B 61 MET cc_start: 0.9036 (ppp) cc_final: 0.8800 (ppp) REVERT: B 124 TYR cc_start: 0.9114 (m-80) cc_final: 0.8862 (m-80) REVERT: G 38 MET cc_start: 0.8575 (ttp) cc_final: 0.8221 (ttm) REVERT: N 89 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7905 (pt0) outliers start: 40 outliers final: 23 residues processed: 174 average time/residue: 0.6006 time to fit residues: 110.9049 Evaluate side-chains 167 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 120 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 ASN R 227 GLN A 31 GLN A 292 ASN A 357 HIS B 17 GLN N 1 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.168510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120098 restraints weight = 9750.011| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.98 r_work: 0.3057 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9568 Z= 0.138 Angle : 0.550 9.705 12905 Z= 0.285 Chirality : 0.043 0.209 1413 Planarity : 0.004 0.056 1620 Dihedral : 7.674 68.107 1481 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.65 % Allowed : 17.85 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.25), residues: 1138 helix: 1.66 (0.25), residues: 447 sheet: -0.11 (0.32), residues: 239 loop : -0.36 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 105 TYR 0.012 0.001 TYR R 149 PHE 0.013 0.001 PHE A 212 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9558) covalent geometry : angle 0.54356 / 0.28 (12885) SS BOND : bond 0.00386 / 0.27 ( 7) SS BOND : angle 2.44780 / 1.99 ( 14) hydrogen bonds : bond 0.04241 / 2.87 ( 459) hydrogen bonds : angle 4.50817 / 3.24 ( 1311) Misc. bond : bond 0.00005 / 0.00 ( 1) link_NAG-ASN : bond 0.00458 / 0.24 ( 2) link_NAG-ASN : angle 1.14437 / 0.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.218 Fit side-chains REVERT: R 140 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6775 (tp30) REVERT: R 196 MET cc_start: 0.8396 (mtt) cc_final: 0.8063 (mtp) REVERT: R 204 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6343 (mm-30) REVERT: R 229 MET cc_start: 0.8706 (mmp) cc_final: 0.8355 (mmp) REVERT: R 284 TYR cc_start: 0.7296 (m-80) cc_final: 0.7064 (m-80) REVERT: R 405 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7056 (tm-30) REVERT: A 17 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6820 (pttt) REVERT: A 19 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: A 221 MET cc_start: 0.9083 (ttp) cc_final: 0.8850 (ttp) REVERT: A 299 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6606 (tt0) REVERT: A 356 ARG cc_start: 0.7573 (mtm110) cc_final: 0.7350 (mtm110) REVERT: A 358 TYR cc_start: 0.8533 (m-80) cc_final: 0.8143 (m-80) REVERT: B 19 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7275 (ttp80) REVERT: B 57 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8739 (pttp) REVERT: B 61 MET cc_start: 0.9057 (ppp) cc_final: 0.8798 (ppp) REVERT: B 124 TYR cc_start: 0.9104 (m-80) cc_final: 0.8870 (m-80) REVERT: B 219 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8094 (mtm180) REVERT: G 38 MET cc_start: 0.8555 (ttp) cc_final: 0.8210 (ttm) REVERT: N 89 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7878 (pt0) outliers start: 44 outliers final: 23 residues processed: 167 average time/residue: 0.6169 time to fit residues: 109.2730 Evaluate side-chains 169 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 120 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 ASN R 227 GLN A 31 GLN A 292 ASN A 357 HIS B 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.168346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119147 restraints weight = 9745.408| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.05 r_work: 0.3044 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9568 Z= 0.144 Angle : 0.552 8.698 12905 Z= 0.287 Chirality : 0.043 0.211 1413 Planarity : 0.004 0.060 1620 Dihedral : 7.812 67.703 1481 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.33 % Allowed : 18.90 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.25), residues: 1138 helix: 1.76 (0.25), residues: 447 sheet: -0.15 (0.32), residues: 240 loop : -0.32 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 105 TYR 0.013 0.001 TYR B 59 PHE 0.019 0.001 PHE R 172 TRP 0.016 0.002 TRP R 236 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 9558) covalent geometry : angle 0.54641 / 0.28 (12885) SS BOND : bond 0.00351 / 0.23 ( 7) SS BOND : angle 2.32258 / 1.92 ( 14) hydrogen bonds : bond 0.04276 / 2.90 ( 459) hydrogen bonds : angle 4.48846 / 3.22 ( 1311) Misc. bond : bond 0.00006 / 0.00 ( 1) link_NAG-ASN : bond 0.00470 / 0.25 ( 2) link_NAG-ASN : angle 1.13663 / 0.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.351 Fit side-chains REVERT: R 140 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6941 (tp30) REVERT: R 196 MET cc_start: 0.8455 (mtt) cc_final: 0.8139 (mtp) REVERT: R 204 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6810 (mm-30) REVERT: R 284 TYR cc_start: 0.7306 (m-80) cc_final: 0.7023 (m-80) REVERT: A 17 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6879 (pttt) REVERT: A 19 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7790 (mt0) REVERT: A 299 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6616 (tt0) REVERT: A 358 TYR cc_start: 0.8580 (m-80) cc_final: 0.8202 (m-80) REVERT: B 19 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7328 (ttp80) REVERT: B 61 MET cc_start: 0.9080 (ppp) cc_final: 0.8745 (ppp) REVERT: B 124 TYR cc_start: 0.9121 (m-80) cc_final: 0.8901 (m-80) REVERT: B 219 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8128 (mtm180) REVERT: G 38 MET cc_start: 0.8583 (ttp) cc_final: 0.8246 (ttm) REVERT: N 89 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: N 105 ARG cc_start: 0.7245 (ttp-110) cc_final: 0.6950 (mpp80) outliers start: 41 outliers final: 24 residues processed: 166 average time/residue: 0.6863 time to fit residues: 120.7930 Evaluate side-chains 167 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.1980 chunk 105 optimal weight: 0.0670 chunk 11 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 96 optimal weight: 0.0770 chunk 63 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 overall best weight: 0.9878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 3 ASN R 227 GLN A 31 GLN A 292 ASN A 357 HIS A 390 GLN B 17 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.169656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120431 restraints weight = 9667.241| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.94 r_work: 0.3079 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9568 Z= 0.121 Angle : 0.529 9.142 12905 Z= 0.274 Chirality : 0.042 0.210 1413 Planarity : 0.004 0.050 1620 Dihedral : 7.583 68.543 1481 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.70 % Allowed : 19.64 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.25), residues: 1138 helix: 1.89 (0.25), residues: 447 sheet: -0.10 (0.32), residues: 238 loop : -0.27 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 105 TYR 0.013 0.001 TYR R 149 PHE 0.012 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9558) covalent geometry : angle 0.52445 / 0.27 (12885) SS BOND : bond 0.00295 / 0.20 ( 7) SS BOND : angle 2.03068 / 1.66 ( 14) hydrogen bonds : bond 0.03997 / 2.70 ( 459) hydrogen bonds : angle 4.38849 / 3.16 ( 1311) Misc. bond : bond 0.00005 / 0.00 ( 1) link_NAG-ASN : bond 0.00468 / 0.24 ( 2) link_NAG-ASN : angle 1.10536 / 0.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.346 Fit side-chains REVERT: R 140 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6842 (tp30) REVERT: R 196 MET cc_start: 0.8412 (mtt) cc_final: 0.8095 (mtp) REVERT: R 204 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6294 (mm-30) REVERT: R 284 TYR cc_start: 0.7416 (m-80) cc_final: 0.7099 (m-80) REVERT: A 17 LYS cc_start: 0.7496 (ttmm) cc_final: 0.6864 (pttt) REVERT: A 19 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7699 (mt0) REVERT: A 299 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6662 (tt0) REVERT: B 19 ARG cc_start: 0.7870 (ttp80) cc_final: 0.7301 (ttp80) REVERT: B 61 MET cc_start: 0.8945 (ppp) cc_final: 0.8597 (ppp) REVERT: B 219 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8125 (mtm180) REVERT: G 20 LYS cc_start: 0.8176 (mttp) cc_final: 0.7842 (mtpt) REVERT: G 38 MET cc_start: 0.8550 (ttp) cc_final: 0.8204 (ttm) REVERT: N 89 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7903 (pt0) outliers start: 35 outliers final: 22 residues processed: 169 average time/residue: 0.6715 time to fit residues: 120.4190 Evaluate side-chains 168 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 100 optimal weight: 0.0970 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 227 GLN A 31 GLN A 292 ASN A 357 HIS A 390 GLN B 17 GLN G 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.171188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122625 restraints weight = 9663.293| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.12 r_work: 0.3112 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9568 Z= 0.107 Angle : 0.518 10.500 12905 Z= 0.266 Chirality : 0.041 0.213 1413 Planarity : 0.004 0.062 1620 Dihedral : 7.221 69.259 1481 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.85 % Allowed : 20.49 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.25), residues: 1138 helix: 2.16 (0.25), residues: 441 sheet: -0.09 (0.32), residues: 243 loop : -0.14 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 105 TYR 0.011 0.001 TYR R 149 PHE 0.011 0.001 PHE A 212 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 9558) covalent geometry : angle 0.51457 / 0.26 (12885) SS BOND : bond 0.00277 / 0.19 ( 7) SS BOND : angle 1.79721 / 1.42 ( 14) hydrogen bonds : bond 0.03745 / 2.52 ( 459) hydrogen bonds : angle 4.25976 / 3.07 ( 1311) Misc. bond : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : bond 0.00462 / 0.24 ( 2) link_NAG-ASN : angle 1.04623 / 0.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.342 Fit side-chains REVERT: R 140 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7019 (tp30) REVERT: R 196 MET cc_start: 0.8413 (mtt) cc_final: 0.8121 (mtp) REVERT: R 204 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6323 (mm-30) REVERT: R 284 TYR cc_start: 0.7423 (m-80) cc_final: 0.7106 (m-80) REVERT: A 17 LYS cc_start: 0.7498 (ttmm) cc_final: 0.6879 (pttt) REVERT: A 299 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6634 (tt0) REVERT: B 19 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7339 (ttp80) REVERT: B 61 MET cc_start: 0.8927 (ppp) cc_final: 0.8587 (ppp) REVERT: B 219 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8144 (mtm180) REVERT: B 340 ASN cc_start: 0.8341 (t160) cc_final: 0.7928 (t0) REVERT: G 20 LYS cc_start: 0.8217 (mttp) cc_final: 0.7882 (mtpt) REVERT: G 38 MET cc_start: 0.8518 (ttp) cc_final: 0.8202 (ttm) REVERT: N 87 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8057 (mtmt) REVERT: N 89 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7910 (pt0) REVERT: N 105 ARG cc_start: 0.7291 (ttp-110) cc_final: 0.6976 (mpp80) outliers start: 27 outliers final: 17 residues processed: 165 average time/residue: 0.6884 time to fit residues: 120.4646 Evaluate side-chains 159 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 227 GLN A 31 GLN A 292 ASN A 357 HIS A 390 GLN B 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.167249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118362 restraints weight = 9724.981| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.87 r_work: 0.3048 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9568 Z= 0.187 Angle : 0.601 9.173 12905 Z= 0.311 Chirality : 0.045 0.212 1413 Planarity : 0.004 0.067 1620 Dihedral : 8.027 66.296 1481 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.75 % Allowed : 21.01 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.25), residues: 1138 helix: 1.85 (0.25), residues: 446 sheet: -0.13 (0.32), residues: 239 loop : -0.27 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 105 TYR 0.017 0.002 TYR B 59 PHE 0.021 0.002 PHE R 172 TRP 0.016 0.002 TRP R 236 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 ( 9558) covalent geometry : angle 0.59545 / 0.31 (12885) SS BOND : bond 0.00346 / 0.21 ( 7) SS BOND : angle 2.38934 / 2.06 ( 14) hydrogen bonds : bond 0.04588 / 3.13 ( 459) hydrogen bonds : angle 4.53683 / 3.26 ( 1311) Misc. bond : bond 0.00007 / 0.00 ( 1) link_NAG-ASN : bond 0.00470 / 0.25 ( 2) link_NAG-ASN : angle 1.12108 / 0.61 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.361 Fit side-chains REVERT: R 140 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6953 (tp30) REVERT: R 196 MET cc_start: 0.8443 (mtt) cc_final: 0.8126 (mtp) REVERT: R 204 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6778 (mm-30) REVERT: R 229 MET cc_start: 0.8729 (mmt) cc_final: 0.8412 (mmp) REVERT: R 284 TYR cc_start: 0.7424 (m-80) cc_final: 0.7089 (m-80) REVERT: R 405 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7233 (tm-30) REVERT: A 17 LYS cc_start: 0.7544 (ttmm) cc_final: 0.6915 (pttt) REVERT: A 299 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6684 (tt0) REVERT: B 19 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7297 (ttp80) REVERT: B 61 MET cc_start: 0.9129 (ppp) cc_final: 0.8778 (ppp) REVERT: G 38 MET cc_start: 0.8596 (ttp) cc_final: 0.8321 (ttm) REVERT: N 89 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: N 105 ARG cc_start: 0.7249 (ttp-110) cc_final: 0.6934 (mpp80) outliers start: 26 outliers final: 20 residues processed: 160 average time/residue: 0.6602 time to fit residues: 111.9352 Evaluate side-chains 160 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 227 GLN A 31 GLN A 292 ASN A 357 HIS A 390 GLN B 17 GLN N 1 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.170260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121672 restraints weight = 9605.663| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.10 r_work: 0.3085 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9568 Z= 0.116 Angle : 0.530 9.672 12905 Z= 0.272 Chirality : 0.042 0.212 1413 Planarity : 0.004 0.060 1620 Dihedral : 7.475 68.533 1481 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.53 % Allowed : 21.44 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.25), residues: 1138 helix: 2.14 (0.25), residues: 441 sheet: -0.14 (0.32), residues: 239 loop : -0.17 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 105 TYR 0.013 0.001 TYR A 358 PHE 0.011 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9558) covalent geometry : angle 0.52639 / 0.27 (12885) SS BOND : bond 0.00276 / 0.18 ( 7) SS BOND : angle 1.81413 / 1.45 ( 14) hydrogen bonds : bond 0.03872 / 2.62 ( 459) hydrogen bonds : angle 4.29993 / 3.10 ( 1311) Misc. bond : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : bond 0.00463 / 0.24 ( 2) link_NAG-ASN : angle 1.04821 / 0.57 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4208.86 seconds wall clock time: 72 minutes 18.76 seconds (4338.76 seconds total)