Starting phenix.real_space_refine on Tue Mar 3 18:24:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f1r_31423/03_2026/7f1r_31423.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f1r_31423/03_2026/7f1r_31423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f1r_31423/03_2026/7f1r_31423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f1r_31423/03_2026/7f1r_31423.map" model { file = "/net/cci-nas-00/data/ceres_data/7f1r_31423/03_2026/7f1r_31423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f1r_31423/03_2026/7f1r_31423.cif" } resolution = 3.0 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 Anisotropic ADP refinement not supported. Converting 1639 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4274 2.51 5 N 1110 2.21 5 O 1185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.00s 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: 6621 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2450 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 4 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 9, 'ARG:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 4, 'TRP:plan': 1, 'TYR:plan': 3, 'ASP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "A" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1627 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 11, 'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2305 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 239 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 30} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 1.42, per 1000 atoms: 0.21 Number of scatterers: 6621 At special positions: 0 Unit cell: (114.95, 121.22, 68.97, 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 52 16.00 O 1185 8.00 N 1110 7.00 C 4274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 10 " - pdb=" SG CYS R 34 " distance=2.03 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 28 " - pdb=" SG CYS R 267 " distance=2.03 Simple disulfide: pdb=" SG CYS R 196 " - pdb=" SG CYS R 273 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 249.0 milliseconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 43.2% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 3 through 7 Processing helix chain 'R' and resid 56 through 65 removed outlier: 4.064A pdb=" N LEU R 65 " --> pdb=" O TYR R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 153 removed outlier: 3.589A pdb=" N VAL R 146 " --> pdb=" O GLY R 142 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU R 150 " --> pdb=" O VAL R 146 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 176 removed outlier: 4.249A pdb=" N ILE R 162 " --> pdb=" O SER R 158 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR R 163 " --> pdb=" O MET R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 185 Processing helix chain 'R' and resid 193 through 226 Processing helix chain 'R' and resid 227 through 235 Processing helix chain 'R' and resid 236 through 261 Proline residue: R 257 - end of helix Processing helix chain 'R' and resid 281 through 317 removed outlier: 5.314A pdb=" N LEU R 300 " --> pdb=" O LEU R 296 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 321 through 356 removed outlier: 3.606A pdb=" N ARG R 325 " --> pdb=" O ASN R 321 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS R 326 " --> pdb=" O GLU R 322 " (cutoff:3.500A) Proline residue: R 345 - end of helix removed outlier: 3.679A pdb=" N PHE R 355 " --> pdb=" O LEU R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 394 removed outlier: 4.074A pdb=" N ARG R 369 " --> pdb=" O SER R 365 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU R 370 " --> pdb=" O SER R 366 " (cutoff:3.500A) Proline residue: R 389 - end of helix Processing helix chain 'R' and resid 396 through 408 removed outlier: 3.727A pdb=" N TYR R 402 " --> pdb=" O LYS R 398 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU R 403 " --> pdb=" O PHE R 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 33 removed outlier: 3.660A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.626A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 272 through 281 removed outlier: 4.388A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.882A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.697A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.509A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.655A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.557A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 262 through 263 removed outlier: 3.911A pdb=" N ARG R 263 " --> pdb=" O SER R 274 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER R 274 " --> pdb=" O ARG R 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.507A pdb=" N MET A 198 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.984A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.524A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.910A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.433A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.349A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.629A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.860A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 975 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: 1.10 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2094 1.35 - 1.46: 1715 1.46 - 1.58: 2883 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 6762 Sorted by residual: bond pdb=" N ARG A 313 " pdb=" CA ARG A 313 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.27e-02 6.20e+03 5.48e+00 bond pdb=" N ARG B 304 " pdb=" CA ARG B 304 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.22e-02 6.72e+03 4.43e+00 bond pdb=" CA SER R 1 " pdb=" C SER R 1 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.10e-02 2.27e+03 7.37e-01 bond pdb=" CA LEU R 128 " pdb=" C LEU R 128 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.10e-02 2.27e+03 6.53e-01 bond pdb=" C PRO R 129 " pdb=" N PRO R 130 " ideal model delta sigma weight residual 1.336 1.345 -0.009 1.20e-02 6.94e+03 5.79e-01 ... (remaining 6757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 9005 1.32 - 2.64: 158 2.64 - 3.96: 29 3.96 - 5.28: 9 5.28 - 6.60: 5 Bond angle restraints: 9206 Sorted by residual: angle pdb=" N GLN R 281 " pdb=" CA GLN R 281 " pdb=" C GLN R 281 " ideal model delta sigma weight residual 110.44 107.09 3.35 1.20e+00 6.94e-01 7.80e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 121.54 126.67 -5.13 1.91e+00 2.74e-01 7.20e+00 angle pdb=" CA ARG A 313 " pdb=" C ARG A 313 " pdb=" O ARG A 313 " ideal model delta sigma weight residual 120.54 118.15 2.39 1.04e+00 9.25e-01 5.29e+00 angle pdb=" N VAL R 178 " pdb=" CA VAL R 178 " pdb=" C VAL R 178 " ideal model delta sigma weight residual 108.88 113.21 -4.33 2.16e+00 2.14e-01 4.01e+00 angle pdb=" CA VAL R 178 " pdb=" C VAL R 178 " pdb=" N PRO R 179 " ideal model delta sigma weight residual 118.88 121.94 -3.06 1.54e+00 4.22e-01 3.95e+00 ... (remaining 9201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.64: 3652 15.64 - 31.28: 236 31.28 - 46.92: 44 46.92 - 62.55: 10 62.55 - 78.19: 5 Dihedral angle restraints: 3947 sinusoidal: 1343 harmonic: 2604 Sorted by residual: dihedral pdb=" CB CYS R 196 " pdb=" SG CYS R 196 " pdb=" SG CYS R 273 " pdb=" CB CYS R 273 " ideal model delta sinusoidal sigma weight residual -86.00 -161.48 75.48 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS R 28 " pdb=" SG CYS R 28 " pdb=" SG CYS R 267 " pdb=" CB CYS R 267 " ideal model delta sinusoidal sigma weight residual -86.00 -35.92 -50.08 1 1.00e+01 1.00e-02 3.44e+01 dihedral pdb=" CB CYS R 11 " pdb=" SG CYS R 11 " pdb=" SG CYS R 50 " pdb=" CB CYS R 50 " ideal model delta sinusoidal sigma weight residual -86.00 -56.15 -29.85 1 1.00e+01 1.00e-02 1.27e+01 ... (remaining 3944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 643 0.025 - 0.050: 258 0.050 - 0.074: 119 0.074 - 0.099: 53 0.099 - 0.124: 25 Chirality restraints: 1098 Sorted by residual: chirality pdb=" CA LEU R 256 " pdb=" N LEU R 256 " pdb=" C LEU R 256 " pdb=" CB LEU R 256 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA ARG A 313 " pdb=" N ARG A 313 " pdb=" C ARG A 313 " pdb=" CB ARG A 313 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.55e-01 ... (remaining 1095 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 256 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO R 257 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 257 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 257 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 128 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.29e+00 pdb=" N PRO R 129 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO R 129 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 129 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 303 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C ASP B 303 " -0.022 2.00e-02 2.50e+03 pdb=" O ASP B 303 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG B 304 " 0.008 2.00e-02 2.50e+03 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1092 2.76 - 3.29: 6494 3.29 - 3.83: 11101 3.83 - 4.36: 12892 4.36 - 4.90: 22626 Nonbonded interactions: 54205 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.224 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.256 3.040 nonbonded pdb=" O LEU R 150 " pdb=" N ARG R 155 " model vdw 2.266 3.120 nonbonded pdb=" OE1 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.279 3.040 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.321 3.120 ... (remaining 54200 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.500 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 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 : 0.002 0.030 6766 Z= 0.110 Angle : 0.485 6.596 9214 Z= 0.284 Chirality : 0.038 0.124 1098 Planarity : 0.003 0.039 1148 Dihedral : 11.209 78.194 2243 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.46 % Allowed : 1.83 % Favored : 97.71 % 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: -2.21 (0.24), residues: 872 helix: -1.30 (0.23), residues: 354 sheet: -0.71 (0.44), residues: 138 loop : -1.81 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.005 0.001 TYR R 27 PHE 0.006 0.001 PHE B 234 TRP 0.004 0.001 TRP B 339 HIS 0.002 0.000 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 6762) covalent geometry : angle 0.48414 ( 9206) SS BOND : bond 0.00254 ( 4) SS BOND : angle 1.24411 ( 8) hydrogen bonds : bond 0.24447 ( 337) hydrogen bonds : angle 7.65837 ( 975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 195 MET cc_start: 0.7307 (tmm) cc_final: 0.7011 (tmm) REVERT: R 369 ARG cc_start: 0.5788 (mmm-85) cc_final: 0.4496 (tpt170) REVERT: A 198 MET cc_start: 0.7252 (mpp) cc_final: 0.6982 (mpt) REVERT: A 267 PHE cc_start: 0.7686 (m-10) cc_final: 0.7310 (m-10) REVERT: A 296 TYR cc_start: 0.7637 (t80) cc_final: 0.7281 (t80) outliers start: 3 outliers final: 0 residues processed: 158 average time/residue: 0.4670 time to fit residues: 78.0723 Evaluate side-chains 111 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.0980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 GLN ** R 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.182387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.146174 restraints weight = 7554.624| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.14 r_work: 0.3675 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6766 Z= 0.144 Angle : 0.593 8.521 9214 Z= 0.298 Chirality : 0.042 0.164 1098 Planarity : 0.004 0.035 1148 Dihedral : 3.334 13.208 941 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.68 % Allowed : 15.75 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.27), residues: 872 helix: 0.59 (0.27), residues: 354 sheet: -0.50 (0.40), residues: 163 loop : -1.28 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 251 TYR 0.015 0.001 TYR A 230 PHE 0.012 0.001 PHE R 136 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6762) covalent geometry : angle 0.59295 ( 9206) SS BOND : bond 0.00733 ( 4) SS BOND : angle 0.85791 ( 8) hydrogen bonds : bond 0.03913 ( 337) hydrogen bonds : angle 5.02961 ( 975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.232 Fit side-chains REVERT: R 195 MET cc_start: 0.7265 (tmm) cc_final: 0.6868 (tmm) REVERT: R 236 THR cc_start: 0.7274 (p) cc_final: 0.6993 (m) REVERT: R 369 ARG cc_start: 0.6253 (mmm-85) cc_final: 0.4563 (tpt170) REVERT: A 14 GLU cc_start: 0.7878 (tp30) cc_final: 0.7540 (tm-30) REVERT: A 296 TYR cc_start: 0.7934 (t80) cc_final: 0.7405 (t80) REVERT: B 137 ARG cc_start: 0.6396 (OUTLIER) cc_final: 0.6023 (ptp-110) outliers start: 11 outliers final: 5 residues processed: 137 average time/residue: 0.4711 time to fit residues: 68.2902 Evaluate side-chains 118 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 161 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.177151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.138177 restraints weight = 7282.420| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.12 r_work: 0.3580 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6766 Z= 0.178 Angle : 0.608 7.123 9214 Z= 0.312 Chirality : 0.043 0.157 1098 Planarity : 0.004 0.037 1148 Dihedral : 3.692 12.825 941 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.89 % Allowed : 18.20 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.28), residues: 872 helix: 1.23 (0.27), residues: 357 sheet: -0.31 (0.41), residues: 165 loop : -1.08 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 251 TYR 0.012 0.001 TYR A 230 PHE 0.013 0.001 PHE A 189 TRP 0.012 0.002 TRP B 99 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 6762) covalent geometry : angle 0.60777 ( 9206) SS BOND : bond 0.00161 ( 4) SS BOND : angle 0.68592 ( 8) hydrogen bonds : bond 0.03764 ( 337) hydrogen bonds : angle 4.90029 ( 975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: R 151 ILE cc_start: 0.5284 (OUTLIER) cc_final: 0.4836 (pp) REVERT: R 195 MET cc_start: 0.7352 (tmm) cc_final: 0.6850 (tmm) REVERT: R 261 PHE cc_start: 0.7649 (m-10) cc_final: 0.7385 (m-10) REVERT: R 336 MET cc_start: 0.7126 (mtp) cc_final: 0.6822 (mtp) REVERT: R 369 ARG cc_start: 0.6348 (mmm-85) cc_final: 0.4817 (tpt170) REVERT: A 14 GLU cc_start: 0.7845 (tp30) cc_final: 0.7463 (tm-30) REVERT: B 75 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8402 (mm-40) REVERT: B 228 ASP cc_start: 0.7417 (t0) cc_final: 0.7058 (t70) outliers start: 32 outliers final: 9 residues processed: 133 average time/residue: 0.4473 time to fit residues: 63.1771 Evaluate side-chains 115 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 47 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 HIS R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.171710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131493 restraints weight = 7328.917| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.09 r_work: 0.3494 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6766 Z= 0.203 Angle : 0.634 8.680 9214 Z= 0.322 Chirality : 0.044 0.160 1098 Planarity : 0.004 0.038 1148 Dihedral : 3.958 14.292 941 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.35 % Allowed : 19.27 % Favored : 75.38 % 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: 0.17 (0.28), residues: 872 helix: 1.44 (0.27), residues: 357 sheet: -0.45 (0.40), residues: 179 loop : -0.95 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 304 TYR 0.011 0.002 TYR B 124 PHE 0.014 0.002 PHE A 189 TRP 0.016 0.002 TRP B 99 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 6762) covalent geometry : angle 0.63394 ( 9206) SS BOND : bond 0.00165 ( 4) SS BOND : angle 0.52413 ( 8) hydrogen bonds : bond 0.03696 ( 337) hydrogen bonds : angle 4.91015 ( 975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 151 ILE cc_start: 0.5415 (OUTLIER) cc_final: 0.5017 (pp) REVERT: R 195 MET cc_start: 0.7406 (tmm) cc_final: 0.6746 (tmm) REVERT: R 261 PHE cc_start: 0.8081 (m-10) cc_final: 0.7487 (m-10) REVERT: R 369 ARG cc_start: 0.6459 (mmm-85) cc_final: 0.4789 (tpt170) REVERT: A 14 GLU cc_start: 0.7821 (tp30) cc_final: 0.7417 (tm-30) REVERT: A 15 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6312 (ttm170) REVERT: A 186 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: A 202 THR cc_start: 0.8086 (m) cc_final: 0.7848 (p) outliers start: 35 outliers final: 13 residues processed: 135 average time/residue: 0.4820 time to fit residues: 68.9099 Evaluate side-chains 116 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 47 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 72 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 258 ASN R 347 ASN R 384 HIS ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.172599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132739 restraints weight = 7374.197| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.13 r_work: 0.3510 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6766 Z= 0.163 Angle : 0.596 9.074 9214 Z= 0.300 Chirality : 0.042 0.146 1098 Planarity : 0.004 0.039 1148 Dihedral : 3.917 19.064 941 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.05 % Allowed : 20.80 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.29), residues: 872 helix: 1.66 (0.27), residues: 356 sheet: -0.55 (0.40), residues: 174 loop : -0.93 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 251 TYR 0.012 0.001 TYR R 163 PHE 0.010 0.001 PHE R 213 TRP 0.011 0.001 TRP B 99 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6762) covalent geometry : angle 0.59641 ( 9206) SS BOND : bond 0.00366 ( 4) SS BOND : angle 0.41766 ( 8) hydrogen bonds : bond 0.03496 ( 337) hydrogen bonds : angle 4.82916 ( 975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: R 151 ILE cc_start: 0.5705 (OUTLIER) cc_final: 0.5266 (pp) REVERT: R 195 MET cc_start: 0.7365 (tmm) cc_final: 0.6695 (tmm) REVERT: R 261 PHE cc_start: 0.8163 (m-10) cc_final: 0.7906 (m-80) REVERT: R 369 ARG cc_start: 0.6483 (mmm-85) cc_final: 0.4785 (tpt170) REVERT: A 14 GLU cc_start: 0.7783 (tp30) cc_final: 0.7366 (tm-30) REVERT: A 15 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6127 (ttm170) REVERT: A 18 MET cc_start: 0.7949 (tmm) cc_final: 0.7667 (tpp) REVERT: A 186 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: A 202 THR cc_start: 0.8017 (m) cc_final: 0.7765 (p) outliers start: 33 outliers final: 17 residues processed: 121 average time/residue: 0.4615 time to fit residues: 59.2467 Evaluate side-chains 116 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain R residue 402 TYR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 46 optimal weight: 0.0770 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.173591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.134053 restraints weight = 7370.745| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.12 r_work: 0.3522 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6766 Z= 0.144 Angle : 0.582 7.634 9214 Z= 0.293 Chirality : 0.042 0.143 1098 Planarity : 0.004 0.039 1148 Dihedral : 3.847 16.725 941 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.20 % Allowed : 22.17 % Favored : 72.63 % 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: 0.40 (0.29), residues: 872 helix: 1.83 (0.28), residues: 352 sheet: -0.63 (0.40), residues: 170 loop : -0.87 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.021 0.001 TYR R 346 PHE 0.009 0.001 PHE R 213 TRP 0.014 0.002 TRP B 99 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 6762) covalent geometry : angle 0.58179 ( 9206) SS BOND : bond 0.00335 ( 4) SS BOND : angle 0.25383 ( 8) hydrogen bonds : bond 0.03368 ( 337) hydrogen bonds : angle 4.77758 ( 975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: R 151 ILE cc_start: 0.5815 (OUTLIER) cc_final: 0.5392 (pp) REVERT: R 159 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.8050 (tmt) REVERT: R 195 MET cc_start: 0.7347 (tmm) cc_final: 0.6692 (tmm) REVERT: R 369 ARG cc_start: 0.6556 (mmm-85) cc_final: 0.4817 (tpt170) REVERT: A 14 GLU cc_start: 0.7815 (tp30) cc_final: 0.7379 (tm-30) REVERT: A 15 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6330 (ttm170) REVERT: A 18 MET cc_start: 0.7938 (tmm) cc_final: 0.7671 (tpp) REVERT: A 186 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: A 252 SER cc_start: 0.8723 (m) cc_final: 0.8514 (t) outliers start: 34 outliers final: 17 residues processed: 125 average time/residue: 0.4823 time to fit residues: 63.8616 Evaluate side-chains 121 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 402 TYR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 46 optimal weight: 0.0670 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 265 GLN R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.169794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131335 restraints weight = 7484.261| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.15 r_work: 0.3495 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6766 Z= 0.139 Angle : 0.580 8.383 9214 Z= 0.292 Chirality : 0.042 0.146 1098 Planarity : 0.004 0.038 1148 Dihedral : 3.776 15.285 941 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.05 % Allowed : 22.48 % Favored : 72.48 % 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: 0.46 (0.29), residues: 872 helix: 1.94 (0.28), residues: 351 sheet: -0.63 (0.40), residues: 170 loop : -0.86 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.014 0.001 TYR B 124 PHE 0.024 0.001 PHE R 261 TRP 0.013 0.001 TRP B 99 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6762) covalent geometry : angle 0.58002 ( 9206) SS BOND : bond 0.00303 ( 4) SS BOND : angle 0.22618 ( 8) hydrogen bonds : bond 0.03291 ( 337) hydrogen bonds : angle 4.71437 ( 975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: R 151 ILE cc_start: 0.5929 (OUTLIER) cc_final: 0.5545 (pp) REVERT: R 157 LYS cc_start: 0.7585 (mppt) cc_final: 0.7173 (mttt) REVERT: R 159 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7903 (tmt) REVERT: R 195 MET cc_start: 0.7257 (tmm) cc_final: 0.6633 (tmm) REVERT: R 369 ARG cc_start: 0.6584 (mmm-85) cc_final: 0.4891 (tpt170) REVERT: A 14 GLU cc_start: 0.7815 (tp30) cc_final: 0.7370 (tm-30) REVERT: A 15 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6167 (ttm170) REVERT: A 18 MET cc_start: 0.7881 (tmm) cc_final: 0.7588 (tpp) REVERT: A 186 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: A 252 SER cc_start: 0.8745 (m) cc_final: 0.8522 (t) REVERT: B 52 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7737 (mtp85) REVERT: B 264 TYR cc_start: 0.8501 (m-10) cc_final: 0.8252 (m-10) outliers start: 33 outliers final: 18 residues processed: 123 average time/residue: 0.5161 time to fit residues: 66.9419 Evaluate side-chains 122 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 314 LYS Chi-restraints excluded: chain R residue 402 TYR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 265 GLN R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.167475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128769 restraints weight = 7586.048| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.11 r_work: 0.3458 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6766 Z= 0.167 Angle : 0.607 9.697 9214 Z= 0.306 Chirality : 0.042 0.147 1098 Planarity : 0.004 0.038 1148 Dihedral : 3.898 15.729 941 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.20 % Allowed : 23.24 % Favored : 71.56 % 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: 0.44 (0.29), residues: 872 helix: 1.90 (0.28), residues: 351 sheet: -0.68 (0.40), residues: 169 loop : -0.82 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 251 TYR 0.021 0.002 TYR R 346 PHE 0.026 0.001 PHE R 261 TRP 0.016 0.002 TRP B 99 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 6762) covalent geometry : angle 0.60712 ( 9206) SS BOND : bond 0.00315 ( 4) SS BOND : angle 0.30145 ( 8) hydrogen bonds : bond 0.03410 ( 337) hydrogen bonds : angle 4.74871 ( 975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: R 151 ILE cc_start: 0.6099 (OUTLIER) cc_final: 0.5639 (pp) REVERT: R 159 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7979 (tmt) REVERT: R 195 MET cc_start: 0.7283 (tmm) cc_final: 0.6675 (tmm) REVERT: R 318 ARG cc_start: 0.6827 (ppt170) cc_final: 0.6606 (ppt170) REVERT: R 369 ARG cc_start: 0.6667 (mmm-85) cc_final: 0.4998 (tpt170) REVERT: A 14 GLU cc_start: 0.7795 (tp30) cc_final: 0.7334 (tm-30) REVERT: A 15 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6173 (ttm170) REVERT: A 18 MET cc_start: 0.7968 (tmm) cc_final: 0.7683 (tpp) REVERT: A 186 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: A 252 SER cc_start: 0.8725 (m) cc_final: 0.8524 (t) REVERT: B 59 TYR cc_start: 0.8790 (m-80) cc_final: 0.8274 (m-80) REVERT: B 264 TYR cc_start: 0.8603 (m-10) cc_final: 0.8299 (m-10) outliers start: 34 outliers final: 19 residues processed: 121 average time/residue: 0.4815 time to fit residues: 61.6057 Evaluate side-chains 119 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 265 GLN Chi-restraints excluded: chain R residue 402 TYR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 3 optimal weight: 0.0970 chunk 81 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 86 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 265 GLN R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.173938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134677 restraints weight = 7387.299| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.12 r_work: 0.3526 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6766 Z= 0.139 Angle : 0.598 10.650 9214 Z= 0.301 Chirality : 0.042 0.146 1098 Planarity : 0.004 0.038 1148 Dihedral : 3.883 15.728 941 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.59 % Allowed : 24.01 % Favored : 71.41 % 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: 0.50 (0.29), residues: 872 helix: 1.96 (0.28), residues: 351 sheet: -0.66 (0.40), residues: 170 loop : -0.80 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 251 TYR 0.017 0.001 TYR B 124 PHE 0.032 0.001 PHE R 261 TRP 0.013 0.002 TRP B 99 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6762) covalent geometry : angle 0.59866 ( 9206) SS BOND : bond 0.00318 ( 4) SS BOND : angle 0.24879 ( 8) hydrogen bonds : bond 0.03295 ( 337) hydrogen bonds : angle 4.71922 ( 975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: R 151 ILE cc_start: 0.6289 (OUTLIER) cc_final: 0.5871 (pp) REVERT: R 195 MET cc_start: 0.7355 (tmm) cc_final: 0.6750 (tmm) REVERT: R 369 ARG cc_start: 0.6674 (mmm-85) cc_final: 0.5004 (tpt170) REVERT: A 14 GLU cc_start: 0.7879 (tp30) cc_final: 0.7432 (tm-30) REVERT: A 15 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6210 (ttm170) REVERT: A 18 MET cc_start: 0.7944 (tmm) cc_final: 0.7682 (tpp) REVERT: A 186 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7797 (tm-30) REVERT: A 252 SER cc_start: 0.8710 (m) cc_final: 0.8481 (t) REVERT: B 52 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7753 (mtp85) REVERT: B 59 TYR cc_start: 0.8648 (m-80) cc_final: 0.8080 (m-80) REVERT: B 264 TYR cc_start: 0.8577 (m-10) cc_final: 0.8311 (m-10) outliers start: 30 outliers final: 18 residues processed: 117 average time/residue: 0.5270 time to fit residues: 64.9970 Evaluate side-chains 117 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 402 TYR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 3 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 79 optimal weight: 0.3980 chunk 78 optimal weight: 0.5980 chunk 27 optimal weight: 7.9990 chunk 73 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 265 GLN R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.174275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135268 restraints weight = 7319.988| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.11 r_work: 0.3537 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6766 Z= 0.139 Angle : 0.605 10.411 9214 Z= 0.303 Chirality : 0.042 0.139 1098 Planarity : 0.004 0.038 1148 Dihedral : 3.867 15.708 941 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.67 % Allowed : 25.38 % Favored : 70.95 % 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: 0.61 (0.29), residues: 872 helix: 2.00 (0.28), residues: 352 sheet: -0.56 (0.41), residues: 166 loop : -0.72 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 251 TYR 0.022 0.001 TYR R 346 PHE 0.011 0.001 PHE R 136 TRP 0.016 0.002 TRP B 99 HIS 0.004 0.001 HIS R 384 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6762) covalent geometry : angle 0.60550 ( 9206) SS BOND : bond 0.00208 ( 4) SS BOND : angle 0.21924 ( 8) hydrogen bonds : bond 0.03276 ( 337) hydrogen bonds : angle 4.68248 ( 975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: R 151 ILE cc_start: 0.6289 (OUTLIER) cc_final: 0.5872 (pp) REVERT: R 195 MET cc_start: 0.7333 (tmm) cc_final: 0.6722 (tmm) REVERT: R 324 LYS cc_start: 0.8287 (mmpt) cc_final: 0.7601 (mmtm) REVERT: R 369 ARG cc_start: 0.6665 (mmm-85) cc_final: 0.4968 (tpt170) REVERT: A 15 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6239 (ttm170) REVERT: A 18 MET cc_start: 0.7930 (tmm) cc_final: 0.7664 (tpp) REVERT: A 186 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: B 52 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7760 (mtp85) REVERT: B 59 TYR cc_start: 0.8643 (m-80) cc_final: 0.7998 (m-80) outliers start: 24 outliers final: 17 residues processed: 112 average time/residue: 0.5206 time to fit residues: 61.5791 Evaluate side-chains 118 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 402 TYR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 265 GLN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.170786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131385 restraints weight = 7334.887| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.10 r_work: 0.3484 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6766 Z= 0.174 Angle : 0.632 10.296 9214 Z= 0.317 Chirality : 0.042 0.146 1098 Planarity : 0.004 0.039 1148 Dihedral : 4.015 16.163 941 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.98 % Allowed : 25.23 % Favored : 70.80 % 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: 0.48 (0.29), residues: 872 helix: 1.99 (0.27), residues: 347 sheet: -0.68 (0.40), residues: 169 loop : -0.82 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 251 TYR 0.017 0.001 TYR B 124 PHE 0.012 0.001 PHE R 213 TRP 0.018 0.002 TRP B 99 HIS 0.005 0.001 HIS R 384 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6762) covalent geometry : angle 0.63197 ( 9206) SS BOND : bond 0.00245 ( 4) SS BOND : angle 0.32138 ( 8) hydrogen bonds : bond 0.03425 ( 337) hydrogen bonds : angle 4.79517 ( 975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2788.44 seconds wall clock time: 48 minutes 8.90 seconds (2888.90 seconds total)