Starting phenix.real_space_refine on Thu Mar 13 12:51:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f6g_31479/03_2025/7f6g_31479.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f6g_31479/03_2025/7f6g_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_31479/03_2025/7f6g_31479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f6g_31479/03_2025/7f6g_31479.map" model { file = "/net/cci-nas-00/data/ceres_data/7f6g_31479/03_2025/7f6g_31479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f6g_31479/03_2025/7f6g_31479.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.41, per 1000 atoms: 0.62 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: 2.24 Conformation dependent library (CDL) restraints added in 949.4 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: 0.94 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: 2.22 Time building geometry restraints manager: 2.55 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: 5309 23.68 - 47.35: 276 47.35 - 71.03: 32 71.03 - 94.71: 8 94.71 - 118.39: 2 Dihedral angle restraints: 5627 sinusoidal: 2505 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 5624 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 21.920 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 8896 Z= 0.586 Angle : 0.976 8.160 12086 Z= 0.646 Chirality : 0.080 0.487 1385 Planarity : 0.004 0.051 1495 Dihedral : 13.899 118.386 3599 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS B 63 PHE 0.012 0.001 PHE A 110 TYR 0.012 0.001 TYR B 80 ARG 0.003 0.000 ARG A 167 *********************** 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 : 0.981 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: 1.3679 time to fit residues: 223.5495 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 : 0.943 ------------------------------------------------------------------------------- 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 86 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 0.0070 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS B 82 ASN B 88 GLN B 162 ASN B 176 GLN B 287 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.174829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118448 restraints weight = 9317.544| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.65 r_work: 0.3127 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8896 Z= 0.191 Angle : 0.569 7.118 12086 Z= 0.301 Chirality : 0.044 0.187 1385 Planarity : 0.004 0.049 1495 Dihedral : 7.814 71.199 1591 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.26 % Allowed : 10.88 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1050 helix: 1.50 (0.23), residues: 479 sheet: 0.43 (0.37), residues: 189 loop : -1.14 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 339 HIS 0.013 0.001 HIS B 63 PHE 0.012 0.001 PHE A 110 TYR 0.016 0.001 TYR A 312 ARG 0.002 0.000 ARG A 93 *********************** 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 126 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8088 (ttm) REVERT: B 105 HIS cc_start: 0.4933 (OUTLIER) cc_final: 0.4412 (m90) REVERT: B 237 GLN cc_start: 0.7172 (mt0) cc_final: 0.6843 (tt0) REVERT: B 287 HIS cc_start: 0.7521 (m-70) cc_final: 0.7040 (m90) REVERT: B 299 GLN cc_start: 0.7924 (tt0) cc_final: 0.7160 (tm-30) REVERT: B 303 GLN cc_start: 0.7309 (tm-30) cc_final: 0.6829 (tm-30) REVERT: B 356 TYR cc_start: 0.7900 (m-80) cc_final: 0.7624 (m-80) REVERT: C 19 ARG cc_start: 0.7061 (ttp-110) cc_final: 0.6846 (ttm110) REVERT: C 217 MET cc_start: 0.8705 (ptm) cc_final: 0.8339 (ptp) REVERT: C 247 ASP cc_start: 0.7737 (m-30) cc_final: 0.7336 (m-30) REVERT: C 258 ASP cc_start: 0.8183 (t0) cc_final: 0.7262 (t0) outliers start: 21 outliers final: 15 residues processed: 120 average time/residue: 1.2154 time to fit residues: 155.7963 Evaluate side-chains 111 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET 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 359 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 198 LEU 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 73 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4011 r_free = 0.4011 target = 0.174383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119129 restraints weight = 9521.878| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.64 r_work: 0.3132 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8896 Z= 0.185 Angle : 0.520 7.232 12086 Z= 0.275 Chirality : 0.042 0.159 1385 Planarity : 0.004 0.046 1495 Dihedral : 7.418 70.811 1591 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.48 % Allowed : 12.50 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1050 helix: 1.88 (0.24), residues: 482 sheet: 0.55 (0.38), residues: 187 loop : -1.23 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.002 0.001 HIS A 132 PHE 0.013 0.001 PHE A 110 TYR 0.011 0.001 TYR A 312 ARG 0.003 0.000 ARG B 19 *********************** 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 122 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8272 (ttt) cc_final: 0.8023 (ttt) REVERT: B 105 HIS cc_start: 0.4881 (OUTLIER) cc_final: 0.4356 (m90) REVERT: B 237 GLN cc_start: 0.7186 (mt0) cc_final: 0.6879 (tt0) REVERT: B 287 HIS cc_start: 0.7592 (m-70) cc_final: 0.7118 (m90) REVERT: B 299 GLN cc_start: 0.7866 (tt0) cc_final: 0.7136 (tm-30) REVERT: B 303 GLN cc_start: 0.7301 (tm-30) cc_final: 0.6909 (tm-30) REVERT: C 19 ARG cc_start: 0.6990 (ttp-110) cc_final: 0.6789 (ttm110) REVERT: C 247 ASP cc_start: 0.7735 (m-30) cc_final: 0.7305 (m-30) REVERT: C 258 ASP cc_start: 0.8205 (t0) cc_final: 0.7338 (t0) outliers start: 23 outliers final: 13 residues processed: 114 average time/residue: 1.2857 time to fit residues: 155.9850 Evaluate side-chains 101 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 281 ASP Chi-restraints excluded: chain B residue 87 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 333 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 81 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.174320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.119587 restraints weight = 9437.354| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.51 r_work: 0.3135 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 8896 Z= 0.179 Angle : 0.508 7.458 12086 Z= 0.268 Chirality : 0.042 0.134 1385 Planarity : 0.004 0.046 1495 Dihedral : 6.959 70.676 1588 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.34 % Allowed : 13.25 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1050 helix: 1.88 (0.24), residues: 490 sheet: 0.57 (0.38), residues: 187 loop : -1.18 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.002 0.001 HIS A 132 PHE 0.013 0.001 PHE A 110 TYR 0.014 0.001 TYR A 56 ARG 0.002 0.000 ARG A 93 *********************** 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 126 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7948 (ttt) REVERT: A 281 ASP cc_start: 0.7659 (m-30) cc_final: 0.7418 (t0) REVERT: B 105 HIS cc_start: 0.4874 (OUTLIER) cc_final: 0.4137 (m90) REVERT: B 107 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.6082 (mtmt) REVERT: B 237 GLN cc_start: 0.7198 (mt0) cc_final: 0.6878 (tt0) REVERT: B 287 HIS cc_start: 0.7696 (m-70) cc_final: 0.7219 (m90) REVERT: B 299 GLN cc_start: 0.7853 (tt0) cc_final: 0.7110 (tm-30) REVERT: B 303 GLN cc_start: 0.7355 (tm-30) cc_final: 0.6961 (tm-30) REVERT: C 247 ASP cc_start: 0.7745 (m-30) cc_final: 0.7331 (m-30) REVERT: C 258 ASP cc_start: 0.8209 (t0) cc_final: 0.7282 (t0) REVERT: C 262 MET cc_start: 0.8492 (mtp) cc_final: 0.8282 (mtp) outliers start: 31 outliers final: 19 residues processed: 114 average time/residue: 1.2555 time to fit residues: 152.3535 Evaluate side-chains 112 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 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 87 MET 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 186 THR 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 47 THR 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 87 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 85 optimal weight: 0.0770 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.174542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117469 restraints weight = 9432.536| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.79 r_work: 0.3123 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8896 Z= 0.176 Angle : 0.499 7.064 12086 Z= 0.262 Chirality : 0.041 0.130 1385 Planarity : 0.004 0.045 1495 Dihedral : 6.656 70.238 1586 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.34 % Allowed : 14.44 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1050 helix: 1.95 (0.24), residues: 489 sheet: 0.50 (0.38), residues: 189 loop : -1.17 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.002 0.001 HIS C 225 PHE 0.013 0.001 PHE A 110 TYR 0.009 0.001 TYR A 26 ARG 0.004 0.000 ARG C 197 *********************** 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 129 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7776 (ttt) REVERT: A 281 ASP cc_start: 0.7567 (m-30) cc_final: 0.7366 (t0) REVERT: B 105 HIS cc_start: 0.4957 (OUTLIER) cc_final: 0.4499 (m90) REVERT: B 237 GLN cc_start: 0.7176 (mt0) cc_final: 0.6860 (tt0) REVERT: B 287 HIS cc_start: 0.7768 (m-70) cc_final: 0.7290 (m90) REVERT: B 299 GLN cc_start: 0.7881 (tt0) cc_final: 0.7080 (tm-30) REVERT: B 303 GLN cc_start: 0.7283 (tm-30) cc_final: 0.6919 (tm-30) REVERT: C 19 ARG cc_start: 0.6679 (ttm110) cc_final: 0.6468 (ttp-110) REVERT: C 247 ASP cc_start: 0.7746 (m-30) cc_final: 0.7284 (m-30) REVERT: C 258 ASP cc_start: 0.8253 (t0) cc_final: 0.7292 (t0) outliers start: 31 outliers final: 18 residues processed: 114 average time/residue: 1.9763 time to fit residues: 237.6085 Evaluate side-chains 113 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 61 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 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 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 47 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 40 optimal weight: 40.0000 chunk 80 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 4 optimal weight: 0.0000 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.175066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118835 restraints weight = 9394.599| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.71 r_work: 0.3136 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8896 Z= 0.156 Angle : 0.487 7.482 12086 Z= 0.255 Chirality : 0.041 0.146 1385 Planarity : 0.004 0.044 1495 Dihedral : 6.487 69.763 1586 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.91 % Allowed : 15.73 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1050 helix: 2.04 (0.24), residues: 489 sheet: 0.47 (0.38), residues: 192 loop : -1.15 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.002 0.000 HIS L 6 PHE 0.012 0.001 PHE A 110 TYR 0.013 0.001 TYR A 56 ARG 0.004 0.000 ARG D 27 *********************** 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 124 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7739 (ttt) REVERT: B 105 HIS cc_start: 0.4954 (OUTLIER) cc_final: 0.4247 (m90) REVERT: B 107 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6208 (mtmt) REVERT: B 237 GLN cc_start: 0.7178 (mt0) cc_final: 0.6834 (tt0) REVERT: B 303 GLN cc_start: 0.7257 (tm-30) cc_final: 0.6898 (tm-30) REVERT: B 333 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7524 (t0) REVERT: C 247 ASP cc_start: 0.7839 (m-30) cc_final: 0.7287 (m-30) REVERT: C 258 ASP cc_start: 0.8172 (t0) cc_final: 0.7336 (t0) outliers start: 27 outliers final: 17 residues processed: 111 average time/residue: 1.5075 time to fit residues: 177.8036 Evaluate side-chains 114 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 57 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 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 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 C residue 17 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 189 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 67 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN B 287 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.171974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110043 restraints weight = 9540.152| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.55 r_work: 0.3132 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8896 Z= 0.241 Angle : 0.535 7.637 12086 Z= 0.281 Chirality : 0.043 0.133 1385 Planarity : 0.004 0.045 1495 Dihedral : 6.608 69.663 1586 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.45 % Allowed : 15.19 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1050 helix: 1.93 (0.24), residues: 488 sheet: 0.32 (0.38), residues: 196 loop : -1.15 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS A 132 PHE 0.013 0.002 PHE A 110 TYR 0.011 0.001 TYR A 26 ARG 0.005 0.000 ARG D 27 *********************** 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 126 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8152 (ttt) cc_final: 0.7896 (ttt) REVERT: B 105 HIS cc_start: 0.5077 (OUTLIER) cc_final: 0.4698 (m90) REVERT: B 237 GLN cc_start: 0.7318 (mt0) cc_final: 0.7003 (tt0) REVERT: B 303 GLN cc_start: 0.7520 (tm-30) cc_final: 0.7089 (tm-30) REVERT: C 247 ASP cc_start: 0.7963 (m-30) cc_final: 0.7595 (m-30) REVERT: C 258 ASP cc_start: 0.8357 (t0) cc_final: 0.7545 (t0) outliers start: 32 outliers final: 21 residues processed: 114 average time/residue: 1.3357 time to fit residues: 162.1893 Evaluate side-chains 113 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 205 LEU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain B residue 87 MET 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 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 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 47 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 76 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 29 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.173245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111428 restraints weight = 9633.150| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.54 r_work: 0.3150 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8896 Z= 0.197 Angle : 0.516 7.113 12086 Z= 0.270 Chirality : 0.042 0.131 1385 Planarity : 0.004 0.046 1495 Dihedral : 6.206 53.817 1583 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.12 % Allowed : 15.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1050 helix: 1.98 (0.24), residues: 488 sheet: 0.36 (0.37), residues: 194 loop : -1.18 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.002 0.001 HIS A 132 PHE 0.013 0.001 PHE A 110 TYR 0.017 0.001 TYR A 56 ARG 0.006 0.000 ARG C 19 *********************** 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 122 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7647 (ttt) REVERT: B 105 HIS cc_start: 0.5151 (OUTLIER) cc_final: 0.4831 (m90) REVERT: B 237 GLN cc_start: 0.7300 (mt0) cc_final: 0.6988 (tt0) REVERT: B 299 GLN cc_start: 0.7674 (tt0) cc_final: 0.7140 (tp40) REVERT: B 303 GLN cc_start: 0.7372 (tm-30) cc_final: 0.6952 (tm-30) REVERT: C 138 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8202 (mm-30) REVERT: C 247 ASP cc_start: 0.7948 (m-30) cc_final: 0.7564 (m-30) REVERT: C 258 ASP cc_start: 0.8328 (t0) cc_final: 0.7516 (t0) REVERT: C 325 MET cc_start: 0.8963 (mmt) cc_final: 0.8760 (tpp) outliers start: 29 outliers final: 22 residues processed: 109 average time/residue: 1.3543 time to fit residues: 156.8269 Evaluate side-chains 115 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 57 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 205 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain B residue 87 MET 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 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 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 47 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain D residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.173772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117381 restraints weight = 9456.333| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.73 r_work: 0.3113 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8896 Z= 0.185 Angle : 0.520 6.817 12086 Z= 0.272 Chirality : 0.042 0.130 1385 Planarity : 0.004 0.045 1495 Dihedral : 6.121 53.717 1583 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.02 % Allowed : 16.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1050 helix: 2.00 (0.24), residues: 488 sheet: 0.46 (0.38), residues: 190 loop : -1.16 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.002 0.001 HIS B 327 PHE 0.013 0.001 PHE A 110 TYR 0.010 0.001 TYR A 92 ARG 0.008 0.000 ARG C 19 *********************** 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 126 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.7889 (ttt) cc_final: 0.7624 (ttt) REVERT: B 105 HIS cc_start: 0.5154 (OUTLIER) cc_final: 0.4856 (m90) REVERT: B 237 GLN cc_start: 0.7261 (mt0) cc_final: 0.6961 (tt0) REVERT: B 299 GLN cc_start: 0.7507 (tt0) cc_final: 0.7161 (tp-100) REVERT: B 303 GLN cc_start: 0.7184 (tm-30) cc_final: 0.6744 (tm-30) REVERT: C 134 ARG cc_start: 0.6949 (mpt180) cc_final: 0.6748 (mpt180) REVERT: C 138 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8062 (mm-30) REVERT: C 186 ASP cc_start: 0.8581 (m-30) cc_final: 0.8380 (m-30) REVERT: C 247 ASP cc_start: 0.7762 (m-30) cc_final: 0.7336 (m-30) REVERT: C 258 ASP cc_start: 0.8238 (t0) cc_final: 0.7425 (t0) outliers start: 28 outliers final: 20 residues processed: 114 average time/residue: 1.2910 time to fit residues: 156.7535 Evaluate side-chains 117 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 205 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain B residue 87 MET 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 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 47 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain D residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 102 optimal weight: 0.8980 chunk 101 optimal weight: 0.0020 chunk 12 optimal weight: 0.3980 chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 96 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 0.0040 chunk 39 optimal weight: 0.0470 chunk 71 optimal weight: 0.9980 overall best weight: 0.1298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.179204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.118341 restraints weight = 9448.542| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.53 r_work: 0.3236 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8896 Z= 0.129 Angle : 0.493 6.746 12086 Z= 0.258 Chirality : 0.041 0.139 1385 Planarity : 0.004 0.043 1495 Dihedral : 5.559 52.860 1579 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.62 % Allowed : 18.21 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.27), residues: 1050 helix: 2.24 (0.24), residues: 488 sheet: 0.60 (0.39), residues: 182 loop : -1.15 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 219 HIS 0.003 0.000 HIS L 6 PHE 0.015 0.001 PHE B 55 TYR 0.019 0.001 TYR A 56 ARG 0.008 0.000 ARG C 19 ********************** 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 117 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.7763 (ttt) cc_final: 0.7404 (ttt) REVERT: B 105 HIS cc_start: 0.5054 (OUTLIER) cc_final: 0.4765 (m90) REVERT: B 237 GLN cc_start: 0.7346 (mt0) cc_final: 0.7011 (tt0) REVERT: B 299 GLN cc_start: 0.7482 (tt0) cc_final: 0.7009 (tp40) REVERT: B 303 GLN cc_start: 0.7341 (tm-30) cc_final: 0.6995 (tm-30) REVERT: C 138 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8210 (mm-30) REVERT: C 247 ASP cc_start: 0.7988 (m-30) cc_final: 0.7457 (m-30) REVERT: C 258 ASP cc_start: 0.8319 (t0) cc_final: 0.7537 (t0) REVERT: D 20 LYS cc_start: 0.8155 (pttt) cc_final: 0.7895 (pttm) outliers start: 15 outliers final: 10 residues processed: 111 average time/residue: 1.4239 time to fit residues: 170.4094 Evaluate side-chains 103 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 359 VAL Chi-restraints excluded: chain C residue 47 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 71 optimal weight: 0.9980 chunk 102 optimal weight: 0.0670 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4018 r_free = 0.4018 target = 0.175467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118734 restraints weight = 9449.989| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.76 r_work: 0.3125 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8896 Z= 0.183 Angle : 0.535 10.487 12086 Z= 0.276 Chirality : 0.041 0.138 1385 Planarity : 0.004 0.044 1495 Dihedral : 5.671 53.714 1579 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.72 % Allowed : 18.00 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.27), residues: 1050 helix: 2.18 (0.24), residues: 487 sheet: 0.63 (0.39), residues: 188 loop : -1.18 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.002 0.001 HIS A 132 PHE 0.019 0.001 PHE A 28 TYR 0.009 0.001 TYR A 215 ARG 0.011 0.000 ARG C 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6522.24 seconds wall clock time: 113 minutes 44.41 seconds (6824.41 seconds total)