Starting phenix.real_space_refine on Wed Mar 4 02:46:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyn_26188/03_2026/7tyn_26188.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyn_26188/03_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_26188/03_2026/7tyn_26188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyn_26188/03_2026/7tyn_26188.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyn_26188/03_2026/7tyn_26188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyn_26188/03_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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.35, per 1000 atoms: 0.25 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: 0.67 Conformation dependent library (CDL) restraints added in 456.3 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: 0.30 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: 1.33 Time building geometry restraints manager: 0.89 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 - 24.64: 5526 24.64 - 49.29: 233 49.29 - 73.93: 36 73.93 - 98.58: 16 98.58 - 123.22: 1 Dihedral angle restraints: 5812 sinusoidal: 2453 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 5809 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.680 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 13.818 123.221 3621 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 covalent geometry : bond 0.00390 ( 9558) covalent geometry : angle 0.62292 (12885) SS BOND : bond 0.00177 ( 7) SS BOND : angle 1.57224 ( 14) hydrogen bonds : bond 0.25416 ( 459) hydrogen bonds : angle 8.82907 ( 1311) Misc. bond : bond 0.10849 ( 1) link_NAG-ASN : bond 0.00740 ( 2) link_NAG-ASN : angle 3.35769 ( 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 : 0.343 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: 0.7102 (ttmt) REVERT: R 174 ARG cc_start: 0.7704 (mmm-85) cc_final: 0.7390 (mtm-85) REVERT: R 196 MET cc_start: 0.8023 (mtt) cc_final: 0.7744 (mtm) REVERT: R 229 MET cc_start: 0.8624 (tpp) cc_final: 0.8365 (tpp) REVERT: R 230 MET cc_start: 0.8015 (ttm) cc_final: 0.7813 (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: 0.7229 (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: 0.8398 (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: 0.7092 time to fit residues: 152.5067 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 : 0.362 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: R 135 ASN R 179 GLN R 227 GLN R 302 HIS R 383 GLN B 132 ASN B 220 GLN G 24 ASN N 31 ASN 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 = 0.170450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121379 restraints weight = 9600.950| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.99 r_work: 0.3122 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9568 Z= 0.145 Angle : 0.577 8.187 12905 Z= 0.299 Chirality : 0.043 0.233 1413 Planarity : 0.004 0.043 1620 Dihedral : 8.797 107.672 1606 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.38 % Allowed : 16.79 % Favored : 79.83 % 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: -0.74 (0.23), residues: 1138 helix: -0.04 (0.23), residues: 437 sheet: -0.36 (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 0.013 0.001 TYR R 149 PHE 0.017 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 covalent geometry : bond 0.00325 ( 9558) covalent geometry : angle 0.57255 (12885) SS BOND : bond 0.00320 ( 7) SS BOND : angle 2.03678 ( 14) hydrogen bonds : bond 0.04878 ( 459) hydrogen bonds : angle 4.96886 ( 1311) Misc. bond : bond 0.00005 ( 1) link_NAG-ASN : bond 0.00576 ( 2) link_NAG-ASN : angle 1.41757 ( 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 188 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.423 Fit side-chains REVERT: R 112 CYS cc_start: -0.0699 (OUTLIER) cc_final: -0.0995 (m) REVERT: R 140 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6885 (tp30) REVERT: R 174 ARG cc_start: 0.7527 (mmm-85) cc_final: 0.7230 (mtm-85) REVERT: R 204 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6342 (mm-30) REVERT: R 229 MET cc_start: 0.8730 (tpp) cc_final: 0.8407 (mmm) REVERT: R 337 MET cc_start: 0.7658 (ttp) cc_final: 0.7287 (ttm) REVERT: R 405 GLN cc_start: 0.7567 (tm-30) cc_final: 0.7082 (tm-30) REVERT: A 221 MET cc_start: 0.9022 (ttp) cc_final: 0.8791 (ttp) REVERT: A 358 TYR cc_start: 0.8529 (m-80) cc_final: 0.8145 (m-80) REVERT: B 19 ARG cc_start: 0.7793 (ttp80) cc_final: 0.7222 (ttp80) REVERT: B 61 MET cc_start: 0.8901 (ppp) cc_final: 0.8641 (ppp) REVERT: G 14 LYS cc_start: 0.7705 (mtmt) cc_final: 0.7041 (ttmt) REVERT: G 38 MET cc_start: 0.8501 (ttp) cc_final: 0.8119 (ttm) REVERT: N 46 GLU cc_start: 0.8454 (tt0) cc_final: 0.8133 (tt0) REVERT: N 89 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: N 106 ASP cc_start: 0.8602 (p0) cc_final: 0.8376 (p0) outliers start: 32 outliers final: 12 residues processed: 177 average time/residue: 0.6719 time to fit residues: 125.7061 Evaluate side-chains 161 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 5 optimal weight: 40.0000 chunk 40 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN R 408 GLN A 19 GLN A 31 GLN B 17 GLN N 1 GLN N 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.169163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118320 restraints weight = 9240.209| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.26 r_work: 0.3116 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9568 Z= 0.120 Angle : 0.529 9.626 12905 Z= 0.272 Chirality : 0.042 0.203 1413 Planarity : 0.004 0.038 1620 Dihedral : 8.334 102.863 1598 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.06 % Allowed : 18.48 % Favored : 78.46 % 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: 0.22 (0.24), residues: 1138 helix: 1.21 (0.24), residues: 441 sheet: -0.20 (0.32), residues: 234 loop : -0.60 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.011 0.001 TYR R 149 PHE 0.012 0.001 PHE A 212 TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9558) covalent geometry : angle 0.52463 (12885) SS BOND : bond 0.00273 ( 7) SS BOND : angle 1.87243 ( 14) hydrogen bonds : bond 0.04327 ( 459) hydrogen bonds : angle 4.58653 ( 1311) Misc. bond : bond 0.00007 ( 1) link_NAG-ASN : bond 0.00500 ( 2) link_NAG-ASN : angle 1.51113 ( 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 185 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.369 Fit side-chains REVERT: R 196 MET cc_start: 0.8474 (mtt) cc_final: 0.8234 (mtm) REVERT: R 204 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6476 (mm-30) REVERT: R 229 MET cc_start: 0.8746 (tpp) cc_final: 0.8350 (mmm) REVERT: R 327 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8358 (mtt) REVERT: A 221 MET cc_start: 0.9104 (ttp) cc_final: 0.8834 (ttp) REVERT: A 358 TYR cc_start: 0.8562 (m-80) cc_final: 0.8200 (m-80) REVERT: B 19 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7277 (ttp80) REVERT: B 57 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8725 (pttp) REVERT: B 61 MET cc_start: 0.8913 (ppp) cc_final: 0.8703 (ppp) REVERT: B 124 TYR cc_start: 0.9160 (m-80) cc_final: 0.8889 (m-80) REVERT: B 340 ASN cc_start: 0.8145 (t160) cc_final: 0.7626 (t0) REVERT: G 38 MET cc_start: 0.8575 (ttp) cc_final: 0.8124 (ttm) REVERT: N 30 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8713 (p) REVERT: N 89 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8007 (pt0) outliers start: 29 outliers final: 11 residues processed: 171 average time/residue: 0.6262 time to fit residues: 113.5158 Evaluate side-chains 163 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 327 MET Chi-restraints excluded: chain A residue 210 THR 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 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 30 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 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: 5.9990 chunk 106 optimal weight: 0.0970 chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN A 31 GLN B 17 GLN B 88 ASN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.169361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.120256 restraints weight = 9766.098| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.00 r_work: 0.3067 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2229 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= 0.142 Angle : 0.552 8.813 12905 Z= 0.284 Chirality : 0.043 0.162 1413 Planarity : 0.004 0.045 1620 Dihedral : 8.426 94.685 1598 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.12 % Allowed : 17.85 % Favored : 78.04 % 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: 0.53 (0.24), residues: 1138 helix: 1.48 (0.25), residues: 447 sheet: -0.08 (0.33), residues: 230 loop : -0.45 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 105 TYR 0.012 0.001 TYR R 149 PHE 0.019 0.001 PHE R 172 TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9558) covalent geometry : angle 0.54629 (12885) SS BOND : bond 0.00455 ( 7) SS BOND : angle 1.99147 ( 14) hydrogen bonds : bond 0.04385 ( 459) hydrogen bonds : angle 4.53925 ( 1311) Misc. bond : bond 0.00003 ( 1) link_NAG-ASN : bond 0.00304 ( 2) link_NAG-ASN : angle 2.32570 ( 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 186 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.296 Fit side-chains REVERT: R 196 MET cc_start: 0.8460 (mtt) cc_final: 0.8140 (mtp) REVERT: R 204 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6279 (mm-30) REVERT: R 229 MET cc_start: 0.8725 (tpp) cc_final: 0.8346 (mmm) REVERT: R 327 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8443 (mtt) REVERT: A 358 TYR cc_start: 0.8575 (m-80) cc_final: 0.8209 (m-80) REVERT: B 19 ARG cc_start: 0.7879 (ttp80) cc_final: 0.7308 (ttp80) REVERT: B 57 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8698 (pttp) REVERT: B 61 MET cc_start: 0.8944 (ppp) cc_final: 0.8717 (ppp) REVERT: B 124 TYR cc_start: 0.9171 (m-80) cc_final: 0.8907 (m-80) REVERT: B 219 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8037 (mtm180) REVERT: G 38 MET cc_start: 0.8528 (ttp) cc_final: 0.8094 (ttm) REVERT: N 89 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7996 (pt0) outliers start: 39 outliers final: 17 residues processed: 171 average time/residue: 0.6446 time to fit residues: 116.7900 Evaluate side-chains 167 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 327 MET Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 364 SER 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 11 optimal weight: 0.0670 chunk 7 optimal weight: 40.0000 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 135 ASN R 227 GLN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN 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 = 0.3899 r_free = 0.3899 target = 0.169283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120674 restraints weight = 9701.718| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.88 r_work: 0.3119 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2345 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= 0.143 Angle : 0.560 9.694 12905 Z= 0.287 Chirality : 0.043 0.176 1413 Planarity : 0.004 0.044 1620 Dihedral : 8.466 88.162 1598 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.01 % Allowed : 18.27 % Favored : 77.72 % 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 (0.24), residues: 1138 helix: 1.67 (0.25), residues: 447 sheet: -0.06 (0.33), residues: 230 loop : -0.39 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 105 TYR 0.013 0.001 TYR R 149 PHE 0.013 0.001 PHE A 212 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9558) covalent geometry : angle 0.55194 (12885) SS BOND : bond 0.00380 ( 7) SS BOND : angle 2.44504 ( 14) hydrogen bonds : bond 0.04312 ( 459) hydrogen bonds : angle 4.50528 ( 1311) Misc. bond : bond 0.00005 ( 1) link_NAG-ASN : bond 0.00338 ( 2) link_NAG-ASN : angle 2.32436 ( 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 185 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.307 Fit side-chains REVERT: R 140 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6915 (tp30) REVERT: R 196 MET cc_start: 0.8456 (mtt) cc_final: 0.8135 (mtp) REVERT: R 204 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6375 (mm-30) REVERT: R 229 MET cc_start: 0.8703 (tpp) cc_final: 0.8294 (mmm) REVERT: R 327 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8399 (mtt) REVERT: A 299 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6432 (tt0) REVERT: B 19 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7338 (ttp80) REVERT: B 57 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8701 (pttp) REVERT: B 61 MET cc_start: 0.9007 (ppp) cc_final: 0.8757 (ppp) REVERT: B 124 TYR cc_start: 0.9145 (m-80) cc_final: 0.8883 (m-80) REVERT: G 38 MET cc_start: 0.8578 (ttp) cc_final: 0.8145 (ttm) REVERT: N 89 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7992 (pt0) outliers start: 38 outliers final: 20 residues processed: 173 average time/residue: 0.6466 time to fit residues: 118.4264 Evaluate side-chains 168 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 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 R residue 327 MET Chi-restraints excluded: chain R residue 334 GLU 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 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 N residue 12 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 357 HIS B 17 GLN N 1 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.169937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121805 restraints weight = 9738.079| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.98 r_work: 0.3081 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2460 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= 0.126 Angle : 0.542 9.728 12905 Z= 0.276 Chirality : 0.042 0.170 1413 Planarity : 0.004 0.049 1620 Dihedral : 8.186 78.339 1598 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.91 % Allowed : 18.27 % Favored : 77.82 % 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: 0.85 (0.24), residues: 1138 helix: 1.84 (0.25), residues: 447 sheet: -0.03 (0.33), residues: 229 loop : -0.33 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 105 TYR 0.014 0.001 TYR N 95 PHE 0.012 0.001 PHE A 212 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9558) covalent geometry : angle 0.53454 (12885) SS BOND : bond 0.00325 ( 7) SS BOND : angle 2.10751 ( 14) hydrogen bonds : bond 0.04052 ( 459) hydrogen bonds : angle 4.37749 ( 1311) Misc. bond : bond 0.00005 ( 1) link_NAG-ASN : bond 0.00259 ( 2) link_NAG-ASN : angle 2.71126 ( 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 185 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.375 Fit side-chains REVERT: R 140 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6840 (tp30) REVERT: R 196 MET cc_start: 0.8347 (mtt) cc_final: 0.8003 (mtp) REVERT: R 204 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6255 (mm-30) REVERT: R 229 MET cc_start: 0.8701 (tpp) cc_final: 0.8303 (mmm) REVERT: R 327 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8327 (mtt) REVERT: A 17 LYS cc_start: 0.7439 (ttmm) cc_final: 0.6751 (pttt) REVERT: A 299 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6317 (tt0) REVERT: A 356 ARG cc_start: 0.7508 (mtm110) cc_final: 0.7278 (mtm110) REVERT: B 19 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7207 (ttp80) REVERT: B 57 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8662 (pttp) REVERT: B 61 MET cc_start: 0.8929 (ppp) cc_final: 0.8675 (ppp) REVERT: B 124 TYR cc_start: 0.9100 (m-80) cc_final: 0.8841 (m-80) REVERT: B 219 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8084 (mtm180) REVERT: G 38 MET cc_start: 0.8521 (ttp) cc_final: 0.8147 (ttm) REVERT: N 87 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7973 (mtpt) REVERT: N 89 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7996 (pt0) outliers start: 37 outliers final: 22 residues processed: 170 average time/residue: 0.6606 time to fit residues: 118.7484 Evaluate side-chains 173 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 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 327 MET Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 210 THR 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 28 THR 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 113 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 122 THR 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: 3.9990 chunk 108 optimal weight: 4.9990 chunk 10 optimal weight: 50.0000 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN R 377 HIS ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 213 GLN A 292 ASN A 294 GLN A 357 HIS B 17 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116534 restraints weight = 9691.452| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.09 r_work: 0.3072 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9568 Z= 0.194 Angle : 0.612 9.633 12905 Z= 0.315 Chirality : 0.045 0.181 1413 Planarity : 0.004 0.059 1620 Dihedral : 8.844 81.099 1598 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 : 4.22 % Allowed : 18.37 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.24), residues: 1138 helix: 1.68 (0.25), residues: 446 sheet: -0.11 (0.32), residues: 234 loop : -0.39 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 105 TYR 0.017 0.002 TYR B 59 PHE 0.019 0.002 PHE R 172 TRP 0.015 0.002 TRP R 236 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 9558) covalent geometry : angle 0.60273 (12885) SS BOND : bond 0.00358 ( 7) SS BOND : angle 2.51041 ( 14) hydrogen bonds : bond 0.04746 ( 459) hydrogen bonds : angle 4.61803 ( 1311) Misc. bond : bond 0.00009 ( 1) link_NAG-ASN : bond 0.00238 ( 2) link_NAG-ASN : angle 3.30462 ( 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 184 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.358 Fit side-chains REVERT: R 140 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7080 (tp30) REVERT: R 196 MET cc_start: 0.8502 (mtt) cc_final: 0.8162 (mtp) REVERT: R 204 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6421 (mm-30) REVERT: R 405 GLN cc_start: 0.7515 (tm-30) cc_final: 0.7014 (tm-30) REVERT: A 299 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6430 (tt0) REVERT: A 356 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7447 (mtm110) REVERT: B 57 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8689 (pttp) REVERT: B 61 MET cc_start: 0.9091 (ppp) cc_final: 0.8744 (ppp) REVERT: B 219 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8105 (mtm180) REVERT: G 38 MET cc_start: 0.8628 (ttp) cc_final: 0.8330 (ttm) REVERT: N 89 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7933 (pt0) REVERT: N 105 ARG cc_start: 0.7028 (ttp-110) cc_final: 0.6783 (mpp80) outliers start: 40 outliers final: 25 residues processed: 172 average time/residue: 0.6836 time to fit residues: 124.2679 Evaluate side-chains 171 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 306 MET Chi-restraints excluded: chain R residue 334 GLU 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 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 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 28 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 98 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3900 r_free = 0.3900 target = 0.169314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.120294 restraints weight = 9635.785| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.08 r_work: 0.3110 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2595 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= 0.131 Angle : 0.549 9.417 12905 Z= 0.282 Chirality : 0.042 0.173 1413 Planarity : 0.004 0.045 1620 Dihedral : 8.226 77.563 1598 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.91 % Allowed : 19.11 % Favored : 76.98 % 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: 0.93 (0.25), residues: 1138 helix: 1.99 (0.25), residues: 441 sheet: -0.16 (0.32), residues: 239 loop : -0.23 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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 covalent geometry : bond 0.00293 ( 9558) covalent geometry : angle 0.53965 (12885) SS BOND : bond 0.00277 ( 7) SS BOND : angle 2.02902 ( 14) hydrogen bonds : bond 0.04069 ( 459) hydrogen bonds : angle 4.40071 ( 1311) Misc. bond : bond 0.00006 ( 1) link_NAG-ASN : bond 0.00140 ( 2) link_NAG-ASN : angle 3.77183 ( 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 180 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.316 Fit side-chains REVERT: R 140 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6976 (tp30) REVERT: R 196 MET cc_start: 0.8456 (mtt) cc_final: 0.8122 (mtp) REVERT: R 204 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6364 (mm-30) REVERT: A 17 LYS cc_start: 0.7584 (ttmm) cc_final: 0.6918 (pttt) REVERT: A 299 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6513 (tt0) REVERT: A 356 ARG cc_start: 0.7586 (mtm110) cc_final: 0.7368 (mtm110) REVERT: B 61 MET cc_start: 0.9026 (ppp) cc_final: 0.8767 (ppp) REVERT: B 124 TYR cc_start: 0.9087 (m-80) cc_final: 0.8879 (m-80) REVERT: B 219 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8132 (mtm180) REVERT: G 38 MET cc_start: 0.8584 (ttp) cc_final: 0.8230 (ttm) REVERT: N 89 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7923 (pt0) outliers start: 37 outliers final: 25 residues processed: 170 average time/residue: 0.6803 time to fit residues: 122.1945 Evaluate side-chains 171 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR 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 28 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 0.2980 chunk 82 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 0.0050 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3913 r_free = 0.3913 target = 0.170505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.122084 restraints weight = 9640.750| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.97 r_work: 0.3138 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9568 Z= 0.115 Angle : 0.531 10.887 12905 Z= 0.272 Chirality : 0.041 0.172 1413 Planarity : 0.004 0.058 1620 Dihedral : 7.835 76.386 1598 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.17 % Allowed : 20.06 % 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: 1.03 (0.25), residues: 1138 helix: 2.06 (0.25), residues: 447 sheet: -0.11 (0.32), residues: 239 loop : -0.20 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 105 TYR 0.012 0.001 TYR R 149 PHE 0.011 0.001 PHE A 212 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9558) covalent geometry : angle 0.52181 (12885) SS BOND : bond 0.00262 ( 7) SS BOND : angle 1.81140 ( 14) hydrogen bonds : bond 0.03856 ( 459) hydrogen bonds : angle 4.28406 ( 1311) Misc. bond : bond 0.00006 ( 1) link_NAG-ASN : bond 0.00134 ( 2) link_NAG-ASN : angle 3.66539 ( 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 173 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.333 Fit side-chains REVERT: R 140 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7024 (tp30) REVERT: R 196 MET cc_start: 0.8434 (mtt) cc_final: 0.8118 (mtp) REVERT: R 204 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6322 (mm-30) REVERT: A 17 LYS cc_start: 0.7525 (ttmm) cc_final: 0.6885 (pttt) REVERT: A 299 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6504 (tt0) REVERT: B 61 MET cc_start: 0.8915 (ppp) cc_final: 0.8569 (ppp) REVERT: B 219 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8124 (mtm180) REVERT: G 20 LYS cc_start: 0.8223 (mttp) cc_final: 0.7894 (mtpt) REVERT: G 38 MET cc_start: 0.8554 (ttp) cc_final: 0.8204 (ttm) REVERT: N 87 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8087 (mtmt) REVERT: N 89 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7800 (pt0) outliers start: 30 outliers final: 21 residues processed: 165 average time/residue: 0.6578 time to fit residues: 115.0140 Evaluate side-chains 163 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR 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 N residue 12 VAL Chi-restraints excluded: chain N residue 28 THR 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 Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 106 optimal weight: 0.0040 chunk 34 optimal weight: 3.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3886 r_free = 0.3886 target = 0.168147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118871 restraints weight = 9724.754| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.13 r_work: 0.3088 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9568 Z= 0.169 Angle : 0.582 8.102 12905 Z= 0.300 Chirality : 0.044 0.184 1413 Planarity : 0.004 0.068 1620 Dihedral : 8.307 78.191 1598 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.06 % Allowed : 20.49 % Favored : 76.45 % 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: 0.92 (0.25), residues: 1138 helix: 1.93 (0.25), residues: 447 sheet: -0.17 (0.31), residues: 241 loop : -0.20 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 105 TYR 0.015 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 covalent geometry : bond 0.00391 ( 9558) covalent geometry : angle 0.57264 (12885) SS BOND : bond 0.00308 ( 7) SS BOND : angle 2.23073 ( 14) hydrogen bonds : bond 0.04427 ( 459) hydrogen bonds : angle 4.46591 ( 1311) Misc. bond : bond 0.00007 ( 1) link_NAG-ASN : bond 0.00156 ( 2) link_NAG-ASN : angle 3.41684 ( 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 175 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.272 Fit side-chains REVERT: R 196 MET cc_start: 0.8476 (mtt) cc_final: 0.8151 (mtp) REVERT: R 204 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6343 (mm-30) REVERT: R 229 MET cc_start: 0.8683 (mmp) cc_final: 0.8406 (mmp) REVERT: R 405 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7266 (tm-30) REVERT: A 17 LYS cc_start: 0.7588 (ttmm) cc_final: 0.6917 (pttt) REVERT: A 299 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6497 (tt0) REVERT: B 57 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8669 (pttp) REVERT: B 61 MET cc_start: 0.9087 (ppp) cc_final: 0.8736 (ppp) REVERT: B 219 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8116 (mtm180) REVERT: G 38 MET cc_start: 0.8604 (ttp) cc_final: 0.8311 (ttm) REVERT: N 89 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7907 (pt0) outliers start: 29 outliers final: 22 residues processed: 167 average time/residue: 0.7251 time to fit residues: 127.6242 Evaluate side-chains 165 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR 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 28 THR 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: 0.9980 chunk 97 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 40.0000 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.167486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120743 restraints weight = 9557.017| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.76 r_work: 0.3058 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9568 Z= 0.181 Angle : 0.595 8.839 12905 Z= 0.308 Chirality : 0.044 0.184 1413 Planarity : 0.004 0.067 1620 Dihedral : 8.542 78.572 1598 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.27 % Allowed : 20.49 % Favored : 76.24 % 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: 0.87 (0.25), residues: 1138 helix: 1.89 (0.25), residues: 446 sheet: -0.19 (0.32), residues: 241 loop : -0.24 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 105 TYR 0.017 0.002 TYR A 358 PHE 0.014 0.002 PHE A 212 TRP 0.016 0.002 TRP R 236 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9558) covalent geometry : angle 0.58659 (12885) SS BOND : bond 0.00321 ( 7) SS BOND : angle 2.37990 ( 14) hydrogen bonds : bond 0.04521 ( 459) hydrogen bonds : angle 4.51449 ( 1311) Misc. bond : bond 0.00007 ( 1) link_NAG-ASN : bond 0.00155 ( 2) link_NAG-ASN : angle 3.16759 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4544.30 seconds wall clock time: 77 minutes 44.92 seconds (4664.92 seconds total)