Starting phenix.real_space_refine on Thu Jul 2 13:52:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f6g_31479/07_2026/7f6g_31479.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f6g_31479/07_2026/7f6g_31479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f6g_31479/07_2026/7f6g_31479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f6g_31479/07_2026/7f6g_31479.map" model { file = "/net/cci-nas-00/data/ceres_data/7f6g_31479/07_2026/7f6g_31479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f6g_31479/07_2026/7f6g_31479.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7f6g_31479/07_2026/7f6g_31479.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f6g_31479/07_2026/7f6g_31479.cif" } resolution = 2.9 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= 0.003 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 52 5.16 5 C 5631 2.51 5 N 1451 2.21 5 O 1563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8697 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2520 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 12, 'TRANS': 297} Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 72 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2890 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 337} Chain: "C" 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: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 182 Unusual residues: {'CLR': 6, 'NAG': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.12, per 1000 atoms: 0.24 Number of scatterers: 8697 At special positions: 0 Unit cell: (101.4, 100.386, 130.806, 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 1563 8.00 N 1451 7.00 C 5631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 180 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 176 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 429.1 milliseconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 50.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 26 through 56 Proline residue: A 32 - end of helix removed outlier: 3.571A pdb=" N LEU A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 80 removed outlier: 4.331A pdb=" N THR A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 90 removed outlier: 3.683A pdb=" N TRP A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 132 removed outlier: 3.618A pdb=" N ALA A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 4.320A pdb=" N ARG A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 167 Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 189 through 202 removed outlier: 3.807A pdb=" N LEU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 230 Processing helix chain 'A' and resid 234 through 269 removed outlier: 3.635A pdb=" N ILE A 238 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 273 through 292 removed outlier: 4.048A pdb=" N ILE A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 292 through 302 Proline residue: A 299 - end of helix Processing helix chain 'A' and resid 306 through 320 removed outlier: 3.659A pdb=" N LYS A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 36 removed outlier: 3.747A pdb=" N LYS B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 63 removed outlier: 3.526A pdb=" N MET B 59 " --> pdb=" O PHE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 97 removed outlier: 3.797A pdb=" N GLY B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 removed outlier: 4.267A pdb=" N LYS B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.547A pdb=" N ALA B 131 " --> pdb=" O PRO B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 163 through 169 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 212 through 217 removed outlier: 4.227A pdb=" N TRP B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 247 through 261 removed outlier: 3.537A pdb=" N TYR B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 267 removed outlier: 4.415A pdb=" N ASN B 266 " --> pdb=" O TRP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 301 through 316 removed outlier: 3.736A pdb=" N ALA B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 316 " --> pdb=" O MET B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 356 Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 9 through 24 removed outlier: 4.100A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.471A pdb=" N LYS A 12 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 195 removed outlier: 3.509A pdb=" N ILE B 190 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU B 40 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL B 204 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 42 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N SER B 225 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS B 41 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N MET B 227 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU B 43 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU B 229 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU B 45 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N ALA B 231 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE B 226 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE B 272 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE B 228 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN B 274 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 230 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 238 through 239 removed outlier: 3.543A pdb=" N LEU B 239 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU B 245 " --> pdb=" O LEU B 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.512A pdb=" N ILE C 338 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.643A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.860A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.666A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.785A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.390A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.671A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1284 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: 1.24 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2431 1.34 - 1.46: 1762 1.46 - 1.58: 4626 1.58 - 1.70: 0 1.70 - 1.83: 77 Bond restraints: 8896 Sorted by residual: bond pdb=" C10 CLR A 405 " pdb=" C5 CLR A 405 " ideal model delta sigma weight residual 1.519 1.386 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C4 CLR A 405 " pdb=" C5 CLR A 405 " ideal model delta sigma weight residual 1.506 1.380 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C10 CLR A 404 " pdb=" C5 CLR A 404 " ideal model delta sigma weight residual 1.519 1.403 0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C10 CLR A 402 " pdb=" C5 CLR A 402 " ideal model delta sigma weight residual 1.519 1.404 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C10 CLR A 406 " pdb=" C5 CLR A 406 " ideal model delta sigma weight residual 1.519 1.404 0.115 2.00e-02 2.50e+03 3.31e+01 ... (remaining 8891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 10955 1.63 - 3.26: 964 3.26 - 4.90: 118 4.90 - 6.53: 40 6.53 - 8.16: 9 Bond angle restraints: 12086 Sorted by residual: angle pdb=" CA GLY A 97 " pdb=" C GLY A 97 " pdb=" O GLY A 97 " ideal model delta sigma weight residual 122.23 118.06 4.17 6.90e-01 2.10e+00 3.65e+01 angle pdb=" C LYS A 232 " pdb=" CA LYS A 232 " pdb=" CB LYS A 232 " ideal model delta sigma weight residual 110.71 115.64 -4.93 9.40e-01 1.13e+00 2.75e+01 angle pdb=" CA LYS A 232 " pdb=" C LYS A 232 " pdb=" N PRO A 233 " ideal model delta sigma weight residual 118.16 121.29 -3.13 7.00e-01 2.04e+00 2.00e+01 angle pdb=" CA VAL B 184 " pdb=" C VAL B 184 " pdb=" N PRO B 185 " ideal model delta sigma weight residual 119.30 122.77 -3.47 8.10e-01 1.52e+00 1.83e+01 angle pdb=" N LEU B 358 " pdb=" CA LEU B 358 " pdb=" C LEU B 358 " ideal model delta sigma weight residual 112.45 106.63 5.82 1.39e+00 5.18e-01 1.75e+01 ... (remaining 12081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 4988 23.68 - 47.35: 250 47.35 - 71.03: 27 71.03 - 94.71: 3 94.71 - 118.39: 2 Dihedral angle restraints: 5270 sinusoidal: 2148 harmonic: 3122 Sorted by residual: dihedral pdb=" CA SER C 227 " pdb=" C SER C 227 " pdb=" N ASP C 228 " pdb=" CA ASP C 228 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" C10 CLR A 405 " pdb=" C1 CLR A 405 " pdb=" C2 CLR A 405 " pdb=" C3 CLR A 405 " ideal model delta sinusoidal sigma weight residual -56.83 61.56 -118.39 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" CA PHE C 222 " pdb=" C PHE C 222 " pdb=" N THR C 223 " pdb=" CA THR C 223 " ideal model delta harmonic sigma weight residual -180.00 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 5267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1190 0.097 - 0.195: 157 0.195 - 0.292: 18 0.292 - 0.389: 9 0.389 - 0.487: 11 Chirality restraints: 1385 Sorted by residual: chirality pdb=" C14 CLR A 402 " pdb=" C13 CLR A 402 " pdb=" C15 CLR A 402 " pdb=" C8 CLR A 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" C14 CLR A 405 " pdb=" C13 CLR A 405 " pdb=" C15 CLR A 405 " pdb=" C8 CLR A 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.79 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" C14 CLR A 403 " pdb=" C13 CLR A 403 " pdb=" C15 CLR A 403 " pdb=" C8 CLR A 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.47 2.00e-01 2.50e+01 5.41e+00 ... (remaining 1382 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 161 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO A 162 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 162 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 162 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 62 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" C ILE B 62 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE B 62 " 0.013 2.00e-02 2.50e+03 pdb=" N HIS B 63 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 223 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C THR C 223 " -0.033 2.00e-02 2.50e+03 pdb=" O THR C 223 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY C 224 " 0.011 2.00e-02 2.50e+03 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 566 2.74 - 3.28: 8622 3.28 - 3.82: 13616 3.82 - 4.36: 17810 4.36 - 4.90: 29513 Nonbonded interactions: 70127 Sorted by model distance: nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.197 3.040 nonbonded pdb=" O SER C 67 " pdb=" OG SER C 67 " model vdw 2.284 3.040 nonbonded pdb=" NZ LYS A 102 " pdb=" O ILE A 164 " model vdw 2.335 3.120 nonbonded pdb=" OD2 ASP B 236 " pdb=" NZ LYS B 282 " model vdw 2.342 3.120 nonbonded pdb=" O ASP A 278 " pdb=" OG1 THR A 282 " model vdw 2.355 3.040 ... (remaining 70122 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: 1.270 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.390 Find NCS groups from input model: 0.050 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 : 0.009 0.133 8899 Z= 0.562 Angle : 0.976 8.160 12093 Z= 0.646 Chirality : 0.080 0.487 1385 Planarity : 0.004 0.051 1495 Dihedral : 13.575 118.386 3242 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.65 % Allowed : 2.59 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.25), residues: 1050 helix: 0.14 (0.23), residues: 474 sheet: 0.21 (0.38), residues: 190 loop : -1.23 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.012 0.001 TYR B 80 PHE 0.012 0.001 PHE A 110 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00878 / 0.56 ( 8896) covalent geometry : angle 0.97555 / 0.65 (12086) SS BOND : bond 0.00147 / 0.08 ( 2) SS BOND : angle 1.72357 / 0.98 ( 4) hydrogen bonds : bond 0.25446 / 17.50 ( 441) hydrogen bonds : angle 7.17995 / 5.10 ( 1284) link_NAG-ASN : bond 0.00230 / 0.12 ( 1) link_NAG-ASN : angle 1.05535 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 151 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7343 (tt) cc_final: 0.7106 (tt) REVERT: A 99 TYR cc_start: 0.6238 (m-80) cc_final: 0.5510 (m-80) REVERT: B 265 GLN cc_start: 0.7808 (pt0) cc_final: 0.7555 (pt0) REVERT: B 303 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7776 (tm-30) REVERT: C 19 ARG cc_start: 0.7431 (ttp-110) cc_final: 0.7226 (ttm110) REVERT: C 247 ASP cc_start: 0.7316 (m-30) cc_final: 0.7008 (m-30) REVERT: C 258 ASP cc_start: 0.7898 (t0) cc_final: 0.6964 (t0) outliers start: 6 outliers final: 4 residues processed: 154 average time/residue: 0.5908 time to fit residues: 96.2717 Evaluate side-chains 108 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 115 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS B 82 ASN B 88 GLN B 106 ASN B 162 ASN B 176 GLN B 287 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.172286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116460 restraints weight = 9441.787| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.62 r_work: 0.3098 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8899 Z= 0.183 Angle : 0.605 7.104 12093 Z= 0.322 Chirality : 0.045 0.195 1385 Planarity : 0.005 0.052 1495 Dihedral : 7.359 108.909 1234 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.80 % Allowed : 10.45 % Favored : 86.75 % 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: 0.37 (0.25), residues: 1050 helix: 1.33 (0.23), residues: 480 sheet: 0.28 (0.37), residues: 191 loop : -1.17 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 2 TYR 0.015 0.002 TYR A 312 PHE 0.014 0.002 PHE C 234 TRP 0.014 0.001 TRP C 82 HIS 0.014 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 8896) covalent geometry : angle 0.60411 / 0.32 (12086) SS BOND : bond 0.00308 / 0.15 ( 2) SS BOND : angle 1.78483 / 0.90 ( 4) hydrogen bonds : bond 0.06238 / 4.19 ( 441) hydrogen bonds : angle 4.62358 / 3.28 ( 1284) link_NAG-ASN : bond 0.00035 / 0.02 ( 1) link_NAG-ASN : angle 1.07723 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 SER cc_start: 0.8413 (m) cc_final: 0.8169 (p) REVERT: B 105 HIS cc_start: 0.4921 (OUTLIER) cc_final: 0.4403 (m90) REVERT: B 234 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7727 (mm-30) REVERT: B 237 GLN cc_start: 0.7188 (mt0) cc_final: 0.6646 (mt0) REVERT: B 287 HIS cc_start: 0.7526 (m-70) cc_final: 0.7065 (m90) REVERT: B 299 GLN cc_start: 0.7884 (tt0) cc_final: 0.7161 (tm-30) REVERT: B 303 GLN cc_start: 0.7340 (tm-30) cc_final: 0.6896 (tm-30) REVERT: B 333 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7514 (t0) REVERT: C 19 ARG cc_start: 0.7136 (ttp-110) cc_final: 0.6920 (ttm110) REVERT: C 217 MET cc_start: 0.8711 (ptm) cc_final: 0.8325 (ptp) REVERT: C 247 ASP cc_start: 0.7746 (m-30) cc_final: 0.7384 (m-30) REVERT: C 258 ASP cc_start: 0.8280 (t0) cc_final: 0.7321 (t0) outliers start: 26 outliers final: 15 residues processed: 120 average time/residue: 0.5780 time to fit residues: 73.6457 Evaluate side-chains 109 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain D residue 31 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.171812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116137 restraints weight = 9453.947| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.57 r_work: 0.3102 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8899 Z= 0.160 Angle : 0.553 7.577 12093 Z= 0.292 Chirality : 0.043 0.167 1385 Planarity : 0.004 0.051 1495 Dihedral : 7.071 108.083 1234 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.91 % Allowed : 12.50 % Favored : 84.59 % 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: 0.62 (0.26), residues: 1050 helix: 1.68 (0.24), residues: 482 sheet: 0.39 (0.38), residues: 191 loop : -1.27 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 93 TYR 0.018 0.001 TYR A 56 PHE 0.013 0.001 PHE A 110 TRP 0.016 0.001 TRP C 82 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 8896) covalent geometry : angle 0.55237 / 0.29 (12086) SS BOND : bond 0.00160 / 0.08 ( 2) SS BOND : angle 1.61218 / 0.84 ( 4) hydrogen bonds : bond 0.05232 / 3.48 ( 441) hydrogen bonds : angle 4.29548 / 3.05 ( 1284) link_NAG-ASN : bond 0.00156 / 0.08 ( 1) link_NAG-ASN : angle 0.77070 / 0.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7714 (pt0) REVERT: B 105 HIS cc_start: 0.4883 (OUTLIER) cc_final: 0.4349 (m90) REVERT: B 287 HIS cc_start: 0.7602 (m-70) cc_final: 0.7141 (m90) REVERT: B 299 GLN cc_start: 0.7870 (tt0) cc_final: 0.7164 (tm-30) REVERT: B 303 GLN cc_start: 0.7400 (tm-30) cc_final: 0.7032 (tm-30) REVERT: C 217 MET cc_start: 0.8723 (ptm) cc_final: 0.8376 (ptp) REVERT: C 247 ASP cc_start: 0.7733 (m-30) cc_final: 0.7351 (m-30) REVERT: C 258 ASP cc_start: 0.8261 (t0) cc_final: 0.7311 (t0) outliers start: 27 outliers final: 15 residues processed: 114 average time/residue: 0.5242 time to fit residues: 63.6267 Evaluate side-chains 105 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 41 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.172990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118314 restraints weight = 9610.371| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.54 r_work: 0.3119 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8899 Z= 0.128 Angle : 0.521 8.048 12093 Z= 0.275 Chirality : 0.042 0.130 1385 Planarity : 0.004 0.048 1495 Dihedral : 6.589 109.496 1229 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.80 % Allowed : 14.55 % Favored : 82.65 % 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: 0.79 (0.26), residues: 1050 helix: 1.84 (0.24), residues: 483 sheet: 0.50 (0.38), residues: 189 loop : -1.23 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 93 TYR 0.009 0.001 TYR A 26 PHE 0.013 0.001 PHE A 110 TRP 0.014 0.001 TRP C 82 HIS 0.002 0.001 HIS L 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 8896) covalent geometry : angle 0.52004 / 0.27 (12086) SS BOND : bond 0.00341 / 0.16 ( 2) SS BOND : angle 1.35716 / 0.75 ( 4) hydrogen bonds : bond 0.04598 / 3.05 ( 441) hydrogen bonds : angle 4.13358 / 2.96 ( 1284) link_NAG-ASN : bond 0.00096 / 0.05 ( 1) link_NAG-ASN : angle 0.74361 / 0.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7956 (tp) cc_final: 0.7718 (pt) REVERT: A 91 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7691 (pt0) REVERT: B 105 HIS cc_start: 0.4870 (OUTLIER) cc_final: 0.4374 (m90) REVERT: B 237 GLN cc_start: 0.7261 (mt0) cc_final: 0.7028 (tt0) REVERT: B 287 HIS cc_start: 0.7700 (m-70) cc_final: 0.7218 (m90) REVERT: B 299 GLN cc_start: 0.7871 (tt0) cc_final: 0.7116 (tm-30) REVERT: B 303 GLN cc_start: 0.7310 (tm-30) cc_final: 0.6948 (tm-30) REVERT: C 19 ARG cc_start: 0.6794 (ttm110) cc_final: 0.6558 (ttp-110) REVERT: C 247 ASP cc_start: 0.7744 (m-30) cc_final: 0.7327 (m-30) REVERT: C 258 ASP cc_start: 0.8260 (t0) cc_final: 0.7312 (t0) outliers start: 26 outliers final: 17 residues processed: 113 average time/residue: 0.5619 time to fit residues: 67.3100 Evaluate side-chains 108 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.170442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.108680 restraints weight = 9586.167| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.53 r_work: 0.3105 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8899 Z= 0.172 Angle : 0.552 7.616 12093 Z= 0.290 Chirality : 0.043 0.146 1385 Planarity : 0.004 0.049 1495 Dihedral : 6.649 110.078 1229 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.34 % Allowed : 15.62 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.26), residues: 1050 helix: 1.71 (0.24), residues: 489 sheet: 0.27 (0.38), residues: 193 loop : -1.19 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 49 TYR 0.014 0.001 TYR A 56 PHE 0.014 0.002 PHE A 110 TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 8896) covalent geometry : angle 0.55154 / 0.29 (12086) SS BOND : bond 0.00149 / 0.07 ( 2) SS BOND : angle 1.67285 / 0.87 ( 4) hydrogen bonds : bond 0.04938 / 3.27 ( 441) hydrogen bonds : angle 4.16946 / 2.98 ( 1284) link_NAG-ASN : bond 0.00154 / 0.08 ( 1) link_NAG-ASN : angle 0.71926 / 0.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7957 (tp) cc_final: 0.7728 (pt) REVERT: A 91 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7863 (pt0) REVERT: B 105 HIS cc_start: 0.5005 (OUTLIER) cc_final: 0.4516 (m90) REVERT: B 237 GLN cc_start: 0.7343 (mt0) cc_final: 0.7115 (tt0) REVERT: B 287 HIS cc_start: 0.7735 (m-70) cc_final: 0.7254 (m90) REVERT: B 299 GLN cc_start: 0.7937 (tt0) cc_final: 0.7119 (tm-30) REVERT: B 303 GLN cc_start: 0.7401 (tm-30) cc_final: 0.6984 (tm-30) REVERT: C 247 ASP cc_start: 0.7877 (m-30) cc_final: 0.7505 (m-30) REVERT: C 258 ASP cc_start: 0.8373 (t0) cc_final: 0.7501 (t0) outliers start: 31 outliers final: 21 residues processed: 113 average time/residue: 0.6283 time to fit residues: 75.4122 Evaluate side-chains 116 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 18 optimal weight: 0.0770 chunk 46 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.172499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116104 restraints weight = 9496.458| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.72 r_work: 0.3096 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8899 Z= 0.128 Angle : 0.520 7.090 12093 Z= 0.274 Chirality : 0.042 0.131 1385 Planarity : 0.004 0.046 1495 Dihedral : 6.556 110.948 1229 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.12 % Allowed : 16.06 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1050 helix: 1.83 (0.24), residues: 489 sheet: 0.38 (0.38), residues: 191 loop : -1.20 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 19 TYR 0.009 0.001 TYR A 26 PHE 0.013 0.001 PHE A 110 TRP 0.014 0.001 TRP C 82 HIS 0.002 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8896) covalent geometry : angle 0.51908 / 0.27 (12086) SS BOND : bond 0.00092 / 0.04 ( 2) SS BOND : angle 1.25587 / 0.64 ( 4) hydrogen bonds : bond 0.04422 / 2.93 ( 441) hydrogen bonds : angle 4.05917 / 2.91 ( 1284) link_NAG-ASN : bond 0.00134 / 0.07 ( 1) link_NAG-ASN : angle 0.76789 / 0.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7936 (tp) cc_final: 0.7733 (pt) REVERT: A 91 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7676 (pt0) REVERT: B 105 HIS cc_start: 0.5007 (OUTLIER) cc_final: 0.4568 (m90) REVERT: B 237 GLN cc_start: 0.7189 (mt0) cc_final: 0.6946 (tt0) REVERT: B 287 HIS cc_start: 0.7759 (m-70) cc_final: 0.7277 (m90) REVERT: B 299 GLN cc_start: 0.7887 (tt0) cc_final: 0.7101 (tm-30) REVERT: B 303 GLN cc_start: 0.7175 (tm-30) cc_final: 0.6759 (tm-30) REVERT: C 134 ARG cc_start: 0.6717 (mpp-170) cc_final: 0.6339 (mpp80) REVERT: C 247 ASP cc_start: 0.7743 (m-30) cc_final: 0.7338 (m-30) REVERT: C 258 ASP cc_start: 0.8274 (t0) cc_final: 0.7388 (t0) REVERT: C 262 MET cc_start: 0.8594 (mtp) cc_final: 0.8363 (mtp) REVERT: C 325 MET cc_start: 0.8849 (mmt) cc_final: 0.8581 (tpp) outliers start: 29 outliers final: 21 residues processed: 116 average time/residue: 0.6378 time to fit residues: 78.5287 Evaluate side-chains 116 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain D residue 31 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.171390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.109815 restraints weight = 9623.002| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.51 r_work: 0.3124 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8899 Z= 0.150 Angle : 0.534 7.112 12093 Z= 0.280 Chirality : 0.043 0.131 1385 Planarity : 0.004 0.048 1495 Dihedral : 6.571 111.330 1229 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.99 % Allowed : 14.98 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.26), residues: 1050 helix: 1.80 (0.24), residues: 488 sheet: 0.37 (0.38), residues: 189 loop : -1.19 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.015 0.001 TYR A 56 PHE 0.014 0.001 PHE A 110 TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 8896) covalent geometry : angle 0.53383 / 0.28 (12086) SS BOND : bond 0.00175 / 0.08 ( 2) SS BOND : angle 1.42367 / 0.73 ( 4) hydrogen bonds : bond 0.04594 / 3.05 ( 441) hydrogen bonds : angle 4.07367 / 2.92 ( 1284) link_NAG-ASN : bond 0.00167 / 0.09 ( 1) link_NAG-ASN : angle 0.74095 / 0.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7771 (pt0) REVERT: B 105 HIS cc_start: 0.5045 (OUTLIER) cc_final: 0.4648 (m90) REVERT: B 237 GLN cc_start: 0.7290 (mt0) cc_final: 0.7057 (tt0) REVERT: B 287 HIS cc_start: 0.7780 (m-70) cc_final: 0.7302 (m90) REVERT: B 299 GLN cc_start: 0.7928 (tt0) cc_final: 0.7110 (tm-30) REVERT: B 303 GLN cc_start: 0.7313 (tm-30) cc_final: 0.6912 (tm-30) REVERT: C 134 ARG cc_start: 0.6749 (mpp-170) cc_final: 0.6452 (mpt180) REVERT: C 138 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8208 (mm-30) REVERT: C 247 ASP cc_start: 0.7858 (m-30) cc_final: 0.7481 (m-30) REVERT: C 258 ASP cc_start: 0.8386 (t0) cc_final: 0.7516 (t0) REVERT: C 262 MET cc_start: 0.8720 (mtp) cc_final: 0.8478 (mtp) REVERT: C 325 MET cc_start: 0.9015 (mmt) cc_final: 0.8755 (tpp) outliers start: 37 outliers final: 29 residues processed: 118 average time/residue: 0.6378 time to fit residues: 79.9627 Evaluate side-chains 124 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain D residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 4 optimal weight: 0.0870 chunk 33 optimal weight: 0.0970 chunk 79 optimal weight: 2.9990 chunk 102 optimal weight: 0.0370 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 ASN B 58 GLN B 137 ASN C 88 ASN C 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.175907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118817 restraints weight = 9404.481| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.79 r_work: 0.3152 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8899 Z= 0.099 Angle : 0.490 6.994 12093 Z= 0.258 Chirality : 0.041 0.131 1385 Planarity : 0.004 0.043 1495 Dihedral : 6.359 112.015 1229 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.48 % Allowed : 16.59 % Favored : 80.93 % 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: 1.00 (0.26), residues: 1050 helix: 2.03 (0.24), residues: 488 sheet: 0.45 (0.38), residues: 192 loop : -1.11 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 19 TYR 0.008 0.001 TYR B 80 PHE 0.013 0.001 PHE B 55 TRP 0.014 0.001 TRP C 339 HIS 0.003 0.000 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 8896) covalent geometry : angle 0.48940 / 0.26 (12086) SS BOND : bond 0.00218 / 0.10 ( 2) SS BOND : angle 0.82139 / 0.45 ( 4) hydrogen bonds : bond 0.03729 / 2.46 ( 441) hydrogen bonds : angle 3.90280 / 2.82 ( 1284) link_NAG-ASN : bond 0.00088 / 0.05 ( 1) link_NAG-ASN : angle 0.86232 / 0.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7926 (mm-30) REVERT: B 105 HIS cc_start: 0.5086 (OUTLIER) cc_final: 0.4742 (m90) REVERT: B 237 GLN cc_start: 0.7199 (mt0) cc_final: 0.6958 (tt0) REVERT: B 303 GLN cc_start: 0.7073 (tm-30) cc_final: 0.6678 (tm-30) REVERT: B 333 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7463 (t0) REVERT: C 134 ARG cc_start: 0.6666 (mpp-170) cc_final: 0.6273 (mpt-90) REVERT: C 138 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8017 (mm-30) REVERT: C 186 ASP cc_start: 0.8451 (m-30) cc_final: 0.8235 (m-30) REVERT: C 247 ASP cc_start: 0.7733 (m-30) cc_final: 0.7281 (m-30) REVERT: C 258 ASP cc_start: 0.8238 (t0) cc_final: 0.7398 (t0) REVERT: C 262 MET cc_start: 0.8547 (mtp) cc_final: 0.8316 (mtp) outliers start: 23 outliers final: 12 residues processed: 118 average time/residue: 0.5865 time to fit residues: 73.7540 Evaluate side-chains 111 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 338 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 20 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 ASN B 162 ASN B 287 HIS C 88 ASN C 176 GLN C 266 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.173040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110768 restraints weight = 9552.946| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.56 r_work: 0.3139 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8899 Z= 0.135 Angle : 0.530 7.946 12093 Z= 0.277 Chirality : 0.042 0.141 1385 Planarity : 0.004 0.044 1495 Dihedral : 5.802 112.323 1222 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.69 % Allowed : 16.59 % Favored : 80.71 % 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: 0.94 (0.26), residues: 1050 helix: 1.94 (0.24), residues: 488 sheet: 0.44 (0.38), residues: 191 loop : -1.09 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 19 TYR 0.017 0.001 TYR A 56 PHE 0.013 0.001 PHE A 110 TRP 0.015 0.001 TRP C 82 HIS 0.002 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 8896) covalent geometry : angle 0.52983 / 0.28 (12086) SS BOND : bond 0.00153 / 0.07 ( 2) SS BOND : angle 1.50142 / 0.85 ( 4) hydrogen bonds : bond 0.04235 / 2.79 ( 441) hydrogen bonds : angle 3.97394 / 2.86 ( 1284) link_NAG-ASN : bond 0.00201 / 0.11 ( 1) link_NAG-ASN : angle 0.70587 / 0.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 HIS cc_start: 0.5006 (OUTLIER) cc_final: 0.4686 (m90) REVERT: B 237 GLN cc_start: 0.7336 (mt0) cc_final: 0.7082 (tt0) REVERT: B 303 GLN cc_start: 0.7342 (tm-30) cc_final: 0.6958 (tm-30) REVERT: C 134 ARG cc_start: 0.6758 (mpp-170) cc_final: 0.6379 (mpt-90) REVERT: C 138 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8240 (mm-30) REVERT: C 186 ASP cc_start: 0.8744 (m-30) cc_final: 0.8523 (m-30) REVERT: C 247 ASP cc_start: 0.7866 (m-30) cc_final: 0.7460 (m-30) REVERT: C 258 ASP cc_start: 0.8323 (t0) cc_final: 0.7602 (t0) REVERT: C 262 MET cc_start: 0.8691 (mtp) cc_final: 0.8470 (mtp) outliers start: 25 outliers final: 13 residues processed: 108 average time/residue: 0.6030 time to fit residues: 69.1826 Evaluate side-chains 106 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.0570 chunk 8 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 100 optimal weight: 0.0270 chunk 80 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 0.0670 chunk 46 optimal weight: 8.9990 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.175945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114373 restraints weight = 9431.603| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.54 r_work: 0.3180 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8899 Z= 0.105 Angle : 0.516 8.159 12093 Z= 0.268 Chirality : 0.041 0.134 1385 Planarity : 0.004 0.043 1495 Dihedral : 5.668 112.684 1222 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.83 % Allowed : 18.10 % Favored : 80.06 % 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: 1.11 (0.27), residues: 1050 helix: 2.15 (0.24), residues: 483 sheet: 0.51 (0.38), residues: 192 loop : -1.06 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 19 TYR 0.008 0.001 TYR B 80 PHE 0.014 0.001 PHE B 55 TRP 0.013 0.001 TRP C 339 HIS 0.002 0.000 HIS L 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 8896) covalent geometry : angle 0.51540 / 0.27 (12086) SS BOND : bond 0.00083 / 0.04 ( 2) SS BOND : angle 0.99660 / 0.56 ( 4) hydrogen bonds : bond 0.03717 / 2.44 ( 441) hydrogen bonds : angle 3.88217 / 2.80 ( 1284) link_NAG-ASN : bond 0.00155 / 0.08 ( 1) link_NAG-ASN : angle 0.77716 / 0.40 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 HIS cc_start: 0.5117 (OUTLIER) cc_final: 0.4815 (m90) REVERT: B 237 GLN cc_start: 0.7286 (mt0) cc_final: 0.7044 (tt0) REVERT: B 299 GLN cc_start: 0.7477 (tt0) cc_final: 0.6988 (tp40) REVERT: B 303 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6886 (tm-30) REVERT: B 333 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7629 (t0) REVERT: C 134 ARG cc_start: 0.6733 (mpp-170) cc_final: 0.6361 (mpt-90) REVERT: C 138 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8226 (mt-10) REVERT: C 186 ASP cc_start: 0.8632 (m-30) cc_final: 0.8410 (m-30) REVERT: C 247 ASP cc_start: 0.7842 (m-30) cc_final: 0.7425 (m-30) REVERT: C 258 ASP cc_start: 0.8350 (t0) cc_final: 0.7504 (t0) outliers start: 17 outliers final: 12 residues processed: 107 average time/residue: 0.5864 time to fit residues: 66.9570 Evaluate side-chains 105 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 101 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.173885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112053 restraints weight = 9457.448| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.52 r_work: 0.3151 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8899 Z= 0.133 Angle : 0.537 10.683 12093 Z= 0.278 Chirality : 0.042 0.148 1385 Planarity : 0.004 0.044 1495 Dihedral : 5.729 112.880 1222 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.94 % Allowed : 18.21 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.27), residues: 1050 helix: 2.11 (0.24), residues: 482 sheet: 0.47 (0.38), residues: 192 loop : -1.06 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 19 TYR 0.022 0.001 TYR A 56 PHE 0.014 0.001 PHE B 55 TRP 0.014 0.001 TRP C 82 HIS 0.002 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 8896) covalent geometry : angle 0.53683 / 0.28 (12086) SS BOND : bond 0.00141 / 0.07 ( 2) SS BOND : angle 1.39173 / 0.79 ( 4) hydrogen bonds : bond 0.04128 / 2.73 ( 441) hydrogen bonds : angle 3.94078 / 2.84 ( 1284) link_NAG-ASN : bond 0.00192 / 0.10 ( 1) link_NAG-ASN : angle 0.71772 / 0.38 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3136.88 seconds wall clock time: 54 minutes 15.55 seconds (3255.55 seconds total)