Starting phenix.real_space_refine on Tue Mar 3 23:38:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ki0_22882/03_2026/7ki0_22882.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ki0_22882/03_2026/7ki0_22882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ki0_22882/03_2026/7ki0_22882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ki0_22882/03_2026/7ki0_22882.map" model { file = "/net/cci-nas-00/data/ceres_data/7ki0_22882/03_2026/7ki0_22882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ki0_22882/03_2026/7ki0_22882.cif" } resolution = 2.5 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5838 2.51 5 N 1588 2.21 5 O 1762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 9242 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1742 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 236 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3175 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 369} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'WF1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'WF1:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 1.90, per 1000 atoms: 0.21 Number of scatterers: 9242 At special positions: 0 Unit cell: (92.13, 98.77, 170.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1762 8.00 N 1588 7.00 C 5838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 270.9 milliseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 42.5% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.543A 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: 3.507A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.730A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.559A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.532A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.541A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.610A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 34 removed outlier: 3.907A pdb=" N ILE P 29 " --> pdb=" O ALA P 25 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA P 30 " --> pdb=" O LYS P 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.800A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 169 removed outlier: 3.989A pdb=" N ILE R 165 " --> pdb=" O ILE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 204 Processing helix chain 'R' and resid 206 through 215 removed outlier: 3.624A pdb=" N GLN R 211 " --> pdb=" O THR R 207 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS R 212 " --> pdb=" O ALA R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 222 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.902A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 274 removed outlier: 3.587A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 294 through 298 Processing helix chain 'R' and resid 306 through 338 Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 364 through 369 removed outlier: 4.356A pdb=" N PHE R 369 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 371 through 375 Processing helix chain 'R' and resid 376 through 403 removed outlier: 3.542A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 423 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.386A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.428A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.606A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.813A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.733A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.615A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.376A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.678A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.143A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AB3, first strand: chain 'R' and resid 80 through 84 459 hydrogen bonds defined for protein. 1299 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: 1.40 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1489 1.31 - 1.44: 2679 1.44 - 1.56: 5131 1.56 - 1.69: 0 1.69 - 1.82: 72 Bond restraints: 9371 Sorted by residual: bond pdb=" C17 WF1 P 101 " pdb=" N16 WF1 P 101 " ideal model delta sigma weight residual 1.344 1.452 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C PRO R 137 " pdb=" N GLU R 138 " ideal model delta sigma weight residual 1.334 1.385 -0.051 1.27e-02 6.20e+03 1.60e+01 bond pdb=" CA PRO R 55 " pdb=" C PRO R 55 " ideal model delta sigma weight residual 1.514 1.533 -0.019 5.50e-03 3.31e+04 1.20e+01 bond pdb=" C LEU R 118 " pdb=" N PRO R 119 " ideal model delta sigma weight residual 1.332 1.369 -0.037 1.12e-02 7.97e+03 1.11e+01 bond pdb=" CA SER R 219 " pdb=" CB SER R 219 " ideal model delta sigma weight residual 1.534 1.488 0.046 1.45e-02 4.76e+03 1.02e+01 ... (remaining 9366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12029 1.89 - 3.78: 602 3.78 - 5.68: 47 5.68 - 7.57: 15 7.57 - 9.46: 2 Bond angle restraints: 12695 Sorted by residual: angle pdb=" N ALA R 256 " pdb=" CA ALA R 256 " pdb=" C ALA R 256 " ideal model delta sigma weight residual 113.02 106.40 6.62 1.20e+00 6.94e-01 3.05e+01 angle pdb=" C LEU R 118 " pdb=" N PRO R 119 " pdb=" CA PRO R 119 " ideal model delta sigma weight residual 119.98 126.34 -6.36 1.16e+00 7.43e-01 3.01e+01 angle pdb=" N LYS P 26 " pdb=" CA LYS P 26 " pdb=" C LYS P 26 " ideal model delta sigma weight residual 112.41 105.40 7.01 1.30e+00 5.92e-01 2.91e+01 angle pdb=" N THR A 364 " pdb=" CA THR A 364 " pdb=" C THR A 364 " ideal model delta sigma weight residual 113.16 106.73 6.43 1.24e+00 6.50e-01 2.69e+01 angle pdb=" N ASP R 215 " pdb=" CA ASP R 215 " pdb=" C ASP R 215 " ideal model delta sigma weight residual 112.87 106.82 6.05 1.20e+00 6.94e-01 2.54e+01 ... (remaining 12690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.00: 5097 19.00 - 38.00: 374 38.00 - 57.00: 50 57.00 - 76.00: 13 76.00 - 95.00: 8 Dihedral angle restraints: 5542 sinusoidal: 2214 harmonic: 3328 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 1.61 -87.61 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 179.48 -86.48 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CA THR R 105 " pdb=" C THR R 105 " pdb=" N ALA R 106 " pdb=" CA ALA R 106 " ideal model delta harmonic sigma weight residual 180.00 152.23 27.77 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 5539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1128 0.069 - 0.137: 218 0.137 - 0.205: 38 0.205 - 0.274: 5 0.274 - 0.342: 4 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA TYR R 220 " pdb=" N TYR R 220 " pdb=" C TYR R 220 " pdb=" CB TYR R 220 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA VAL R 370 " pdb=" N VAL R 370 " pdb=" C VAL R 370 " pdb=" CB VAL R 370 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA GLU R 292 " pdb=" N GLU R 292 " pdb=" C GLU R 292 " pdb=" CB GLU R 292 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1390 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.039 2.00e-02 2.50e+03 3.07e-02 1.88e+01 pdb=" CG TYR B 59 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 218 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU R 218 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU R 218 " -0.022 2.00e-02 2.50e+03 pdb=" N SER R 219 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 198 " 0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ASP R 198 " -0.057 2.00e-02 2.50e+03 pdb=" O ASP R 198 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA R 199 " 0.019 2.00e-02 2.50e+03 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1379 2.75 - 3.29: 8992 3.29 - 3.83: 15822 3.83 - 4.36: 20259 4.36 - 4.90: 33235 Nonbonded interactions: 79687 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.251 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.255 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR R 235 " pdb=" O TRP R 274 " model vdw 2.304 3.040 ... (remaining 79682 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.360 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:6.660 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: 0.8272 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 9378 Z= 0.420 Angle : 0.873 9.462 12707 Z= 0.606 Chirality : 0.059 0.342 1393 Planarity : 0.004 0.052 1614 Dihedral : 13.735 94.998 3372 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.10 % Allowed : 1.83 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.24), residues: 1119 helix: -0.53 (0.24), residues: 433 sheet: 0.38 (0.34), residues: 238 loop : -0.50 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 197 TYR 0.075 0.002 TYR B 59 PHE 0.017 0.002 PHE B 151 TRP 0.022 0.002 TRP P 31 HIS 0.017 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00698 ( 9371) covalent geometry : angle 0.87212 (12695) SS BOND : bond 0.00411 ( 6) SS BOND : angle 1.52886 ( 12) hydrogen bonds : bond 0.22880 ( 459) hydrogen bonds : angle 8.07223 ( 1299) Misc. bond : bond 0.02011 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6924 (tp30) cc_final: 0.6662 (tp30) REVERT: A 311 TYR cc_start: 0.8499 (m-80) cc_final: 0.8236 (m-80) REVERT: B 10 GLU cc_start: 0.7470 (tt0) cc_final: 0.7150 (tp30) REVERT: B 23 LYS cc_start: 0.8521 (tptm) cc_final: 0.8151 (tppt) REVERT: B 217 MET cc_start: 0.7469 (ppp) cc_final: 0.7159 (ppp) REVERT: B 266 HIS cc_start: 0.7803 (t-170) cc_final: 0.7578 (t70) REVERT: G 17 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7561 (mm-30) REVERT: N 50 ASP cc_start: 0.8333 (p0) cc_final: 0.8049 (p0) REVERT: N 105 ARG cc_start: 0.7534 (mmm-85) cc_final: 0.7128 (mtp85) REVERT: R 139 GLU cc_start: 0.4411 (tt0) cc_final: 0.3562 (mt-10) REVERT: R 140 GLN cc_start: 0.5438 (mt0) cc_final: 0.5042 (tp-100) outliers start: 1 outliers final: 2 residues processed: 149 average time/residue: 0.7885 time to fit residues: 123.1754 Evaluate side-chains 120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain P residue 26 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 213 GLN A 239 ASN B 9 GLN B 17 GLN B 268 ASN N 1 GLN R 82 ASN R 234 GLN R 320 ASN R 338 ASN R 374 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.180557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103318 restraints weight = 9271.191| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.71 r_work: 0.2958 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9378 Z= 0.135 Angle : 0.543 6.689 12707 Z= 0.302 Chirality : 0.042 0.145 1393 Planarity : 0.004 0.051 1614 Dihedral : 6.195 75.391 1272 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.92 % Allowed : 7.75 % Favored : 91.34 % 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: 0.62 (0.25), residues: 1119 helix: 1.35 (0.24), residues: 432 sheet: 0.37 (0.33), residues: 247 loop : -0.41 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.033 0.001 TYR R 148 PHE 0.019 0.001 PHE A 212 TRP 0.021 0.002 TRP R 203 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9371) covalent geometry : angle 0.54287 (12695) SS BOND : bond 0.00279 ( 6) SS BOND : angle 0.85470 ( 12) hydrogen bonds : bond 0.05648 ( 459) hydrogen bonds : angle 4.76502 ( 1299) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.376 Fit side-chains REVERT: A 17 LYS cc_start: 0.6876 (tptp) cc_final: 0.6572 (pptt) REVERT: A 265 ARG cc_start: 0.8717 (mtp180) cc_final: 0.8225 (mtt90) REVERT: A 311 TYR cc_start: 0.8468 (m-80) cc_final: 0.8184 (m-80) REVERT: B 10 GLU cc_start: 0.7325 (tt0) cc_final: 0.6807 (tp30) REVERT: B 23 LYS cc_start: 0.8587 (tptm) cc_final: 0.8037 (ttmt) REVERT: B 134 ARG cc_start: 0.7236 (ptm-80) cc_final: 0.6850 (ppt170) REVERT: B 197 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8095 (mtp-110) REVERT: B 217 MET cc_start: 0.8632 (ppp) cc_final: 0.8104 (ppp) REVERT: B 266 HIS cc_start: 0.8158 (t-170) cc_final: 0.7842 (t70) REVERT: G 17 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7470 (mm-30) REVERT: N 50 ASP cc_start: 0.8699 (p0) cc_final: 0.8450 (p0) REVERT: N 105 ARG cc_start: 0.7623 (mmm-85) cc_final: 0.6934 (mtp85) REVERT: R 140 GLN cc_start: 0.5025 (mt0) cc_final: 0.4548 (tp-100) outliers start: 9 outliers final: 2 residues processed: 130 average time/residue: 0.8060 time to fit residues: 110.0202 Evaluate side-chains 117 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain R residue 347 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 73 optimal weight: 0.0470 chunk 97 optimal weight: 1.9990 chunk 36 optimal weight: 0.0000 chunk 67 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.2880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 390 GLN B 340 ASN N 1 GLN R 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.183409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.107699 restraints weight = 9351.525| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.67 r_work: 0.3021 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9378 Z= 0.101 Angle : 0.469 5.018 12707 Z= 0.258 Chirality : 0.040 0.142 1393 Planarity : 0.003 0.051 1614 Dihedral : 5.227 59.574 1265 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.02 % Allowed : 10.30 % Favored : 88.69 % 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: 1.23 (0.25), residues: 1119 helix: 2.18 (0.24), residues: 429 sheet: 0.41 (0.32), residues: 248 loop : -0.25 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 36 TYR 0.027 0.001 TYR R 148 PHE 0.017 0.001 PHE A 212 TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 9371) covalent geometry : angle 0.46910 (12695) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.56380 ( 12) hydrogen bonds : bond 0.04193 ( 459) hydrogen bonds : angle 4.16544 ( 1299) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6515 (pptt) REVERT: A 265 ARG cc_start: 0.8654 (mtp180) cc_final: 0.8153 (mtt90) REVERT: A 311 TYR cc_start: 0.8363 (m-80) cc_final: 0.8041 (m-80) REVERT: B 23 LYS cc_start: 0.8525 (tptm) cc_final: 0.7957 (ttmt) REVERT: B 134 ARG cc_start: 0.7223 (ptm-80) cc_final: 0.6848 (ppt170) REVERT: B 197 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8055 (mmm-85) REVERT: G 17 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7421 (mm-30) REVERT: G 32 LYS cc_start: 0.8107 (tptp) cc_final: 0.7897 (tmtm) REVERT: N 50 ASP cc_start: 0.8629 (p0) cc_final: 0.8347 (p0) REVERT: N 105 ARG cc_start: 0.7653 (mmm-85) cc_final: 0.6956 (mtm180) REVERT: R 140 GLN cc_start: 0.4899 (mt0) cc_final: 0.4464 (tp40) REVERT: R 221 GLN cc_start: 0.5267 (tm130) cc_final: 0.4938 (mp10) REVERT: R 292 GLU cc_start: 0.6306 (tt0) cc_final: 0.5958 (pp20) REVERT: R 336 LYS cc_start: 0.7235 (ptpt) cc_final: 0.6947 (mtpp) REVERT: R 347 CYS cc_start: 0.5698 (m) cc_final: 0.5125 (t) REVERT: R 408 GLU cc_start: 0.6769 (tt0) cc_final: 0.6316 (mm-30) outliers start: 10 outliers final: 1 residues processed: 124 average time/residue: 0.8289 time to fit residues: 107.9923 Evaluate side-chains 113 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain R residue 68 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 105 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 390 GLN N 1 GLN N 77 ASN R 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.179132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.104335 restraints weight = 9331.769| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.01 r_work: 0.2885 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9378 Z= 0.178 Angle : 0.540 5.986 12707 Z= 0.294 Chirality : 0.042 0.139 1393 Planarity : 0.004 0.050 1614 Dihedral : 5.468 54.207 1265 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.83 % Allowed : 10.91 % Favored : 87.26 % 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: 1.20 (0.25), residues: 1119 helix: 2.12 (0.24), residues: 435 sheet: 0.42 (0.32), residues: 246 loop : -0.28 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.024 0.002 TYR R 148 PHE 0.015 0.002 PHE A 212 TRP 0.017 0.001 TRP A 234 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9371) covalent geometry : angle 0.53969 (12695) SS BOND : bond 0.00367 ( 6) SS BOND : angle 0.78434 ( 12) hydrogen bonds : bond 0.04790 ( 459) hydrogen bonds : angle 4.38847 ( 1299) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6563 (pptt) REVERT: A 265 ARG cc_start: 0.8703 (mtp180) cc_final: 0.8197 (mtt90) REVERT: A 311 TYR cc_start: 0.8450 (m-80) cc_final: 0.8183 (m-80) REVERT: B 23 LYS cc_start: 0.8574 (tptm) cc_final: 0.7982 (ttmt) REVERT: B 134 ARG cc_start: 0.7305 (ptm-80) cc_final: 0.6884 (ppt170) REVERT: B 197 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8042 (mmm-85) REVERT: G 17 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7360 (mm-30) REVERT: G 42 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: N 50 ASP cc_start: 0.8812 (p0) cc_final: 0.8562 (p0) REVERT: N 105 ARG cc_start: 0.7551 (mmm-85) cc_final: 0.6857 (mtm180) REVERT: R 140 GLN cc_start: 0.4967 (mt0) cc_final: 0.4516 (tp40) REVERT: R 221 GLN cc_start: 0.5122 (tm130) cc_final: 0.4743 (mp10) REVERT: R 271 SER cc_start: 0.8287 (OUTLIER) cc_final: 0.7981 (m) REVERT: R 292 GLU cc_start: 0.6404 (tt0) cc_final: 0.5940 (pp20) outliers start: 18 outliers final: 6 residues processed: 116 average time/residue: 0.8637 time to fit residues: 104.9592 Evaluate side-chains 121 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 347 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 78 optimal weight: 40.0000 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 390 GLN N 1 GLN N 35 ASN N 77 ASN R 234 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.179528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.105460 restraints weight = 9232.335| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.98 r_work: 0.2895 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9378 Z= 0.154 Angle : 0.509 5.608 12707 Z= 0.278 Chirality : 0.042 0.135 1393 Planarity : 0.003 0.052 1614 Dihedral : 5.260 48.744 1265 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.14 % Allowed : 11.72 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.25), residues: 1119 helix: 2.26 (0.24), residues: 435 sheet: 0.53 (0.33), residues: 240 loop : -0.28 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 36 TYR 0.024 0.002 TYR R 148 PHE 0.016 0.002 PHE A 212 TRP 0.015 0.001 TRP A 234 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9371) covalent geometry : angle 0.50911 (12695) SS BOND : bond 0.00350 ( 6) SS BOND : angle 0.72004 ( 12) hydrogen bonds : bond 0.04488 ( 459) hydrogen bonds : angle 4.25572 ( 1299) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6531 (pptt) REVERT: A 265 ARG cc_start: 0.8687 (mtp180) cc_final: 0.8182 (mtt90) REVERT: A 311 TYR cc_start: 0.8438 (m-80) cc_final: 0.8188 (m-80) REVERT: B 23 LYS cc_start: 0.8545 (tptm) cc_final: 0.7923 (ttmt) REVERT: B 134 ARG cc_start: 0.7277 (ptm-80) cc_final: 0.6847 (ppt170) REVERT: B 197 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8035 (mmm-85) REVERT: G 17 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7419 (mm-30) REVERT: G 42 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: N 50 ASP cc_start: 0.8803 (p0) cc_final: 0.8549 (p0) REVERT: N 105 ARG cc_start: 0.7555 (mmm-85) cc_final: 0.6860 (mtm180) REVERT: R 140 GLN cc_start: 0.5000 (mt0) cc_final: 0.4539 (tp40) REVERT: R 221 GLN cc_start: 0.5127 (tm130) cc_final: 0.4744 (mp10) REVERT: R 271 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.7941 (m) REVERT: R 292 GLU cc_start: 0.6513 (tt0) cc_final: 0.6034 (pp20) outliers start: 21 outliers final: 7 residues processed: 124 average time/residue: 0.8256 time to fit residues: 107.4644 Evaluate side-chains 121 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 347 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 0.0060 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 390 GLN N 1 GLN N 35 ASN R 234 GLN R 338 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.179106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.104986 restraints weight = 9273.251| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.00 r_work: 0.2888 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9378 Z= 0.163 Angle : 0.518 5.447 12707 Z= 0.282 Chirality : 0.042 0.137 1393 Planarity : 0.004 0.052 1614 Dihedral : 5.184 43.519 1265 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.94 % Allowed : 12.64 % Favored : 85.42 % 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: 1.36 (0.25), residues: 1119 helix: 2.29 (0.24), residues: 435 sheet: 0.54 (0.33), residues: 240 loop : -0.26 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.022 0.002 TYR R 148 PHE 0.016 0.002 PHE A 212 TRP 0.016 0.001 TRP A 234 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9371) covalent geometry : angle 0.51789 (12695) SS BOND : bond 0.00373 ( 6) SS BOND : angle 0.72323 ( 12) hydrogen bonds : bond 0.04521 ( 459) hydrogen bonds : angle 4.25436 ( 1299) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.8696 (mtp180) cc_final: 0.8181 (mtt90) REVERT: A 311 TYR cc_start: 0.8461 (m-80) cc_final: 0.8202 (m-80) REVERT: B 23 LYS cc_start: 0.8563 (tptm) cc_final: 0.7935 (ttmt) REVERT: B 134 ARG cc_start: 0.7259 (ptm-80) cc_final: 0.6833 (ppt170) REVERT: B 197 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8043 (mtp-110) REVERT: G 17 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7388 (mm-30) REVERT: G 42 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: N 50 ASP cc_start: 0.8800 (p0) cc_final: 0.8533 (p0) REVERT: N 105 ARG cc_start: 0.7565 (mmm-85) cc_final: 0.6884 (mtp85) REVERT: R 140 GLN cc_start: 0.5000 (mt0) cc_final: 0.4545 (tp40) REVERT: R 221 GLN cc_start: 0.5188 (tm130) cc_final: 0.4710 (mp-120) REVERT: R 271 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7950 (m) outliers start: 19 outliers final: 10 residues processed: 120 average time/residue: 0.8272 time to fit residues: 104.1461 Evaluate side-chains 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 347 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 390 GLN N 1 GLN N 35 ASN R 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.179646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.105861 restraints weight = 9317.503| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.01 r_work: 0.2901 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9378 Z= 0.138 Angle : 0.496 5.329 12707 Z= 0.271 Chirality : 0.041 0.134 1393 Planarity : 0.003 0.053 1614 Dihedral : 4.985 39.281 1265 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.34 % Allowed : 12.95 % Favored : 84.71 % 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: 1.42 (0.25), residues: 1119 helix: 2.37 (0.24), residues: 435 sheet: 0.51 (0.33), residues: 240 loop : -0.20 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 219 TYR 0.021 0.001 TYR R 148 PHE 0.016 0.001 PHE A 212 TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9371) covalent geometry : angle 0.49550 (12695) SS BOND : bond 0.00313 ( 6) SS BOND : angle 0.66014 ( 12) hydrogen bonds : bond 0.04287 ( 459) hydrogen bonds : angle 4.13909 ( 1299) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.8690 (mtp180) cc_final: 0.8186 (mtt90) REVERT: A 311 TYR cc_start: 0.8438 (m-80) cc_final: 0.8207 (m-80) REVERT: B 23 LYS cc_start: 0.8556 (tptm) cc_final: 0.7946 (ttmt) REVERT: B 134 ARG cc_start: 0.7248 (ptm-80) cc_final: 0.6825 (ppt170) REVERT: B 197 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8051 (mmm-85) REVERT: G 17 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7337 (mm-30) REVERT: G 42 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: N 50 ASP cc_start: 0.8756 (p0) cc_final: 0.8485 (p0) REVERT: N 105 ARG cc_start: 0.7604 (mmm-85) cc_final: 0.6913 (mtm180) REVERT: R 140 GLN cc_start: 0.4979 (mt0) cc_final: 0.4518 (tp40) REVERT: R 197 LYS cc_start: 0.6307 (ttpt) cc_final: 0.5780 (tttt) REVERT: R 221 GLN cc_start: 0.5107 (tm130) cc_final: 0.4614 (mp10) REVERT: R 271 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7949 (m) outliers start: 23 outliers final: 8 residues processed: 125 average time/residue: 0.8332 time to fit residues: 109.4354 Evaluate side-chains 121 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 347 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN N 1 GLN N 35 ASN R 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.180641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107250 restraints weight = 9218.247| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.02 r_work: 0.2928 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9378 Z= 0.114 Angle : 0.475 5.235 12707 Z= 0.261 Chirality : 0.040 0.133 1393 Planarity : 0.003 0.053 1614 Dihedral : 4.748 35.480 1265 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.73 % Allowed : 13.97 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.25), residues: 1119 helix: 2.49 (0.24), residues: 435 sheet: 0.52 (0.33), residues: 239 loop : -0.20 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.021 0.001 TYR R 148 PHE 0.016 0.001 PHE A 212 TRP 0.020 0.001 TRP R 72 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9371) covalent geometry : angle 0.47478 (12695) SS BOND : bond 0.00506 ( 6) SS BOND : angle 0.68497 ( 12) hydrogen bonds : bond 0.04005 ( 459) hydrogen bonds : angle 4.00603 ( 1299) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.8684 (mtp180) cc_final: 0.8178 (mtt90) REVERT: A 311 TYR cc_start: 0.8398 (m-80) cc_final: 0.8126 (m-80) REVERT: A 386 MET cc_start: 0.8996 (ttp) cc_final: 0.8717 (tmm) REVERT: B 23 LYS cc_start: 0.8545 (tptm) cc_final: 0.7981 (ttmt) REVERT: B 59 TYR cc_start: 0.9329 (OUTLIER) cc_final: 0.8434 (t80) REVERT: B 134 ARG cc_start: 0.7254 (ptm-80) cc_final: 0.6843 (ppt170) REVERT: B 172 GLU cc_start: 0.8469 (tp30) cc_final: 0.8258 (tt0) REVERT: B 197 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8047 (mmm-85) REVERT: G 17 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7393 (mm-30) REVERT: N 50 ASP cc_start: 0.8726 (p0) cc_final: 0.8455 (p0) REVERT: N 105 ARG cc_start: 0.7585 (mmm-85) cc_final: 0.6936 (mtm180) REVERT: R 140 GLN cc_start: 0.5015 (mt0) cc_final: 0.4555 (tp40) REVERT: R 221 GLN cc_start: 0.5186 (tm130) cc_final: 0.4666 (mp10) REVERT: R 271 SER cc_start: 0.8170 (OUTLIER) cc_final: 0.7895 (m) outliers start: 17 outliers final: 7 residues processed: 125 average time/residue: 0.8055 time to fit residues: 106.0715 Evaluate side-chains 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 347 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.0170 chunk 104 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN N 1 GLN N 35 ASN R 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.179941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.106587 restraints weight = 9210.412| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.01 r_work: 0.2908 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9378 Z= 0.130 Angle : 0.490 5.310 12707 Z= 0.268 Chirality : 0.041 0.135 1393 Planarity : 0.003 0.052 1614 Dihedral : 4.726 33.542 1265 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.43 % Allowed : 14.78 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.54 (0.25), residues: 1119 helix: 2.46 (0.24), residues: 438 sheet: 0.61 (0.33), residues: 244 loop : -0.19 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.020 0.001 TYR R 148 PHE 0.015 0.001 PHE A 212 TRP 0.016 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9371) covalent geometry : angle 0.48921 (12695) SS BOND : bond 0.00510 ( 6) SS BOND : angle 0.95785 ( 12) hydrogen bonds : bond 0.04149 ( 459) hydrogen bonds : angle 4.04740 ( 1299) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.8693 (mtp180) cc_final: 0.8189 (mtt90) REVERT: A 311 TYR cc_start: 0.8419 (m-80) cc_final: 0.8128 (m-80) REVERT: B 23 LYS cc_start: 0.8528 (tptm) cc_final: 0.7931 (ttmt) REVERT: B 59 TYR cc_start: 0.9333 (OUTLIER) cc_final: 0.8453 (t80) REVERT: B 134 ARG cc_start: 0.7274 (ptm-80) cc_final: 0.6849 (ppt170) REVERT: B 172 GLU cc_start: 0.8478 (tp30) cc_final: 0.8259 (tt0) REVERT: B 197 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8038 (mmm-85) REVERT: B 215 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7832 (mm-30) REVERT: G 17 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7427 (mm-30) REVERT: N 50 ASP cc_start: 0.8745 (p0) cc_final: 0.8456 (p0) REVERT: N 105 ARG cc_start: 0.7614 (mmm-85) cc_final: 0.6918 (mtm180) REVERT: R 140 GLN cc_start: 0.4995 (mt0) cc_final: 0.4512 (tp40) REVERT: R 221 GLN cc_start: 0.5004 (tm130) cc_final: 0.4497 (mp-120) REVERT: R 271 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7924 (m) outliers start: 14 outliers final: 7 residues processed: 121 average time/residue: 0.8052 time to fit residues: 102.5387 Evaluate side-chains 121 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 347 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 0.0050 chunk 69 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN N 1 GLN N 35 ASN R 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.181038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.107707 restraints weight = 9276.469| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.01 r_work: 0.2943 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9378 Z= 0.107 Angle : 0.465 5.527 12707 Z= 0.255 Chirality : 0.040 0.133 1393 Planarity : 0.003 0.052 1614 Dihedral : 4.510 32.119 1265 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.12 % Allowed : 15.29 % Favored : 83.59 % 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: 1.62 (0.26), residues: 1119 helix: 2.55 (0.24), residues: 438 sheet: 0.65 (0.33), residues: 242 loop : -0.17 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.020 0.001 TYR R 148 PHE 0.015 0.001 PHE A 212 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9371) covalent geometry : angle 0.46469 (12695) SS BOND : bond 0.00366 ( 6) SS BOND : angle 0.72604 ( 12) hydrogen bonds : bond 0.03870 ( 459) hydrogen bonds : angle 3.93397 ( 1299) Misc. bond : bond 0.00015 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.8688 (mtp180) cc_final: 0.8162 (mtt90) REVERT: A 311 TYR cc_start: 0.8418 (m-80) cc_final: 0.8147 (m-80) REVERT: A 386 MET cc_start: 0.8996 (ttp) cc_final: 0.8715 (tmm) REVERT: B 23 LYS cc_start: 0.8570 (tptm) cc_final: 0.8013 (ttmt) REVERT: B 59 TYR cc_start: 0.9324 (OUTLIER) cc_final: 0.8449 (t80) REVERT: B 134 ARG cc_start: 0.7230 (ptm-80) cc_final: 0.6823 (ppt170) REVERT: B 172 GLU cc_start: 0.8428 (tp30) cc_final: 0.8217 (tt0) REVERT: B 197 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8034 (mmm-85) REVERT: B 215 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7825 (mm-30) REVERT: G 17 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7375 (mm-30) REVERT: N 50 ASP cc_start: 0.8710 (p0) cc_final: 0.8441 (p0) REVERT: N 105 ARG cc_start: 0.7584 (mmm-85) cc_final: 0.6930 (mtm180) REVERT: R 140 GLN cc_start: 0.5035 (mt0) cc_final: 0.4563 (tp40) REVERT: R 221 GLN cc_start: 0.5072 (tm130) cc_final: 0.4558 (mp-120) REVERT: R 271 SER cc_start: 0.8140 (OUTLIER) cc_final: 0.7875 (m) REVERT: R 411 LEU cc_start: 0.6620 (tp) cc_final: 0.6128 (mt) outliers start: 11 outliers final: 7 residues processed: 121 average time/residue: 0.7454 time to fit residues: 94.8769 Evaluate side-chains 123 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 347 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN N 1 GLN N 35 ASN N 77 ASN R 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.180023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.106469 restraints weight = 9165.670| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.98 r_work: 0.2909 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9378 Z= 0.134 Angle : 0.492 5.320 12707 Z= 0.269 Chirality : 0.041 0.135 1393 Planarity : 0.003 0.052 1614 Dihedral : 4.603 30.198 1265 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.22 % Allowed : 15.19 % Favored : 83.59 % 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: 1.59 (0.25), residues: 1119 helix: 2.50 (0.24), residues: 438 sheet: 0.64 (0.33), residues: 243 loop : -0.16 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.020 0.001 TYR R 148 PHE 0.015 0.001 PHE A 212 TRP 0.015 0.001 TRP A 234 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9371) covalent geometry : angle 0.49143 (12695) SS BOND : bond 0.00410 ( 6) SS BOND : angle 0.82194 ( 12) hydrogen bonds : bond 0.04116 ( 459) hydrogen bonds : angle 4.02871 ( 1299) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5300.33 seconds wall clock time: 90 minutes 31.01 seconds (5431.01 seconds total)