Starting phenix.real_space_refine on Thu Feb 13 10:27:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f6g_31479/02_2025/7f6g_31479.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f6g_31479/02_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_31479/02_2025/7f6g_31479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f6g_31479/02_2025/7f6g_31479.map" model { file = "/net/cci-nas-00/data/ceres_data/7f6g_31479/02_2025/7f6g_31479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f6g_31479/02_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-5592/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: 5.49, per 1000 atoms: 0.63 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.86 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: 2.53 Time building geometry restraints manager: 2.68 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: 0.950 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.450 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- 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 : 0.976 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: 222.9769 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 : 0.971 ------------------------------------------------------------------------------- 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 = 0.174832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118451 restraints weight = 9317.296| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.65 r_work: 0.3130 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 71.198 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 : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8069 (ttm) REVERT: B 105 HIS cc_start: 0.4946 (OUTLIER) cc_final: 0.4430 (m90) REVERT: B 237 GLN cc_start: 0.7142 (mt0) cc_final: 0.6815 (tt0) REVERT: B 287 HIS cc_start: 0.7526 (m-70) cc_final: 0.7031 (m90) REVERT: B 299 GLN cc_start: 0.7943 (tt0) cc_final: 0.7155 (tm-30) REVERT: B 303 GLN cc_start: 0.7265 (tm-30) cc_final: 0.6782 (tm-30) REVERT: B 356 TYR cc_start: 0.7872 (m-80) cc_final: 0.7596 (m-80) REVERT: C 19 ARG cc_start: 0.7038 (ttp-110) cc_final: 0.6821 (ttm110) REVERT: C 217 MET cc_start: 0.8691 (ptm) cc_final: 0.8319 (ptp) REVERT: C 247 ASP cc_start: 0.7728 (m-30) cc_final: 0.7316 (m-30) REVERT: C 258 ASP cc_start: 0.8167 (t0) cc_final: 0.7242 (t0) outliers start: 21 outliers final: 15 residues processed: 120 average time/residue: 1.2767 time to fit residues: 163.1829 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 : 1.030 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.174020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.118561 restraints weight = 9512.493| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.62 r_work: 0.3126 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1950 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= 0.190 Angle : 0.522 7.186 12086 Z= 0.277 Chirality : 0.042 0.158 1385 Planarity : 0.004 0.047 1495 Dihedral : 7.364 70.415 1591 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.69 % Allowed : 12.28 % 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: 1.87 (0.24), residues: 482 sheet: 0.51 (0.38), residues: 189 loop : -1.22 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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: 25 poor density : 97 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8298 (ttt) cc_final: 0.8068 (ttt) REVERT: B 105 HIS cc_start: 0.4880 (OUTLIER) cc_final: 0.4368 (m90) REVERT: B 237 GLN cc_start: 0.7196 (mt0) cc_final: 0.6890 (tt0) REVERT: B 287 HIS cc_start: 0.7594 (m-70) cc_final: 0.7129 (m90) REVERT: B 299 GLN cc_start: 0.7865 (tt0) cc_final: 0.7122 (tm-30) REVERT: B 303 GLN cc_start: 0.7335 (tm-30) cc_final: 0.6949 (tm-30) REVERT: C 247 ASP cc_start: 0.7745 (m-30) cc_final: 0.7311 (m-30) REVERT: C 258 ASP cc_start: 0.8215 (t0) cc_final: 0.7269 (t0) outliers start: 25 outliers final: 14 residues processed: 112 average time/residue: 1.3573 time to fit residues: 161.4042 Evaluate side-chains 103 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 205 LEU 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 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 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 81 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.173568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116827 restraints weight = 9449.875| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.72 r_work: 0.3106 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 0.037 8896 Z= 0.197 Angle : 0.517 7.562 12086 Z= 0.272 Chirality : 0.042 0.137 1385 Planarity : 0.004 0.047 1495 Dihedral : 6.867 70.680 1586 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.23 % Allowed : 13.69 % Favored : 83.08 % 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: 0.83 (0.26), residues: 1050 helix: 1.83 (0.24), residues: 489 sheet: 0.43 (0.38), residues: 191 loop : -1.16 (0.30), residues: 370 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 0.015 0.001 TYR A 56 ARG 0.003 0.000 ARG C 19 *********************** 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 125 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7960 (ttt) REVERT: B 105 HIS cc_start: 0.4945 (OUTLIER) cc_final: 0.4486 (m90) REVERT: B 237 GLN cc_start: 0.7177 (mt0) cc_final: 0.6849 (tt0) REVERT: B 287 HIS cc_start: 0.7708 (m-70) cc_final: 0.7218 (m90) REVERT: B 299 GLN cc_start: 0.7875 (tt0) cc_final: 0.7092 (tm-30) REVERT: B 303 GLN cc_start: 0.7297 (tm-30) cc_final: 0.6927 (tm-30) REVERT: C 19 ARG cc_start: 0.6809 (ttm110) cc_final: 0.6585 (ttp-110) REVERT: C 247 ASP cc_start: 0.7773 (m-30) cc_final: 0.7347 (m-30) REVERT: C 258 ASP cc_start: 0.8223 (t0) cc_final: 0.7273 (t0) outliers start: 30 outliers final: 17 residues processed: 113 average time/residue: 1.3529 time to fit residues: 162.7428 Evaluate side-chains 109 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 190 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 268 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 87 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 0.0270 chunk 6 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.173132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116437 restraints weight = 9461.507| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.73 r_work: 0.3102 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8896 Z= 0.207 Angle : 0.516 7.183 12086 Z= 0.272 Chirality : 0.042 0.131 1385 Planarity : 0.004 0.047 1495 Dihedral : 6.730 70.276 1586 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.56 % Allowed : 14.55 % Favored : 81.90 % 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: 0.86 (0.26), residues: 1050 helix: 1.90 (0.24), residues: 489 sheet: 0.48 (0.38), residues: 189 loop : -1.20 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS C 225 PHE 0.013 0.001 PHE A 110 TYR 0.011 0.001 TYR B 356 ARG 0.002 0.000 ARG C 49 *********************** 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 130 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7792 (ttt) REVERT: B 105 HIS cc_start: 0.4990 (OUTLIER) cc_final: 0.4278 (m90) REVERT: B 107 LYS cc_start: 0.6638 (OUTLIER) cc_final: 0.6208 (mtmt) REVERT: B 237 GLN cc_start: 0.7253 (mt0) cc_final: 0.6957 (tt0) REVERT: B 287 HIS cc_start: 0.7757 (m-70) cc_final: 0.7267 (m90) REVERT: B 299 GLN cc_start: 0.7902 (tt0) cc_final: 0.7088 (tm-30) REVERT: B 303 GLN cc_start: 0.7302 (tm-30) cc_final: 0.6955 (tm-30) REVERT: C 247 ASP cc_start: 0.7749 (m-30) cc_final: 0.7312 (m-30) REVERT: C 258 ASP cc_start: 0.8250 (t0) cc_final: 0.7361 (t0) outliers start: 33 outliers final: 19 residues processed: 115 average time/residue: 1.3895 time to fit residues: 170.7647 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 : 1.199 ------------------------------------------------------------------------------- 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 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 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 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 69 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 40 optimal weight: 40.0000 chunk 80 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.174179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.117798 restraints weight = 9410.403| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.73 r_work: 0.3118 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2371 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= 0.166 Angle : 0.495 6.961 12086 Z= 0.260 Chirality : 0.042 0.152 1385 Planarity : 0.004 0.045 1495 Dihedral : 6.533 69.677 1586 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.02 % Allowed : 15.73 % Favored : 81.25 % 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: 0.92 (0.26), residues: 1050 helix: 1.99 (0.24), residues: 489 sheet: 0.38 (0.38), residues: 192 loop : -1.17 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.002 0.001 HIS L 6 PHE 0.013 0.001 PHE A 110 TYR 0.014 0.001 TYR A 56 ARG 0.005 0.000 ARG C 19 *********************** 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 127 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7796 (ttt) REVERT: B 105 HIS cc_start: 0.4991 (OUTLIER) cc_final: 0.4560 (m90) REVERT: B 237 GLN cc_start: 0.7250 (mt0) cc_final: 0.6920 (tt0) REVERT: B 287 HIS cc_start: 0.7774 (m-70) cc_final: 0.7310 (m90) REVERT: B 299 GLN cc_start: 0.7865 (tt0) cc_final: 0.7095 (tm-30) REVERT: B 303 GLN cc_start: 0.7312 (tm-30) cc_final: 0.6972 (tm-30) REVERT: C 247 ASP cc_start: 0.7769 (m-30) cc_final: 0.7324 (m-30) REVERT: C 258 ASP cc_start: 0.8231 (t0) cc_final: 0.7376 (t0) outliers start: 28 outliers final: 18 residues processed: 116 average time/residue: 1.3166 time to fit residues: 162.4118 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 : 0.965 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 67 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 0.0030 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.174757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118304 restraints weight = 9465.499| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.75 r_work: 0.3126 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8896 Z= 0.164 Angle : 0.498 7.896 12086 Z= 0.261 Chirality : 0.041 0.138 1385 Planarity : 0.004 0.044 1495 Dihedral : 6.411 69.631 1586 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.56 % Allowed : 15.30 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.97 (0.26), residues: 1050 helix: 2.05 (0.24), residues: 488 sheet: 0.42 (0.38), residues: 192 loop : -1.19 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.002 0.001 HIS L 6 PHE 0.013 0.001 PHE A 110 TYR 0.008 0.001 TYR A 26 ARG 0.005 0.000 ARG C 19 *********************** 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 132 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7588 (ttt) REVERT: B 105 HIS cc_start: 0.5035 (OUTLIER) cc_final: 0.4652 (m90) REVERT: B 237 GLN cc_start: 0.7165 (mt0) cc_final: 0.6837 (tt0) REVERT: B 303 GLN cc_start: 0.7213 (tm-30) cc_final: 0.6874 (tm-30) REVERT: B 333 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7532 (t0) REVERT: C 138 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8074 (mm-30) REVERT: C 186 ASP cc_start: 0.8547 (m-30) cc_final: 0.8235 (m-30) REVERT: C 247 ASP cc_start: 0.7762 (m-30) cc_final: 0.7294 (m-30) REVERT: C 258 ASP cc_start: 0.8235 (t0) cc_final: 0.7347 (t0) REVERT: C 262 MET cc_start: 0.8523 (mtp) cc_final: 0.8276 (mtp) REVERT: C 325 MET cc_start: 0.8838 (mmt) cc_final: 0.8614 (tpp) outliers start: 33 outliers final: 22 residues processed: 119 average time/residue: 1.3395 time to fit residues: 169.6608 Evaluate side-chains 118 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 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 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 101 MET Chi-restraints excluded: chain C residue 189 SER 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 76 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 55 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.174638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113006 restraints weight = 9615.658| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.55 r_work: 0.3172 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2535 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= 0.168 Angle : 0.496 7.139 12086 Z= 0.260 Chirality : 0.041 0.133 1385 Planarity : 0.004 0.044 1495 Dihedral : 6.035 53.603 1583 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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 (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: 0.98 (0.26), residues: 1050 helix: 2.06 (0.24), residues: 488 sheet: 0.38 (0.37), residues: 194 loop : -1.17 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.002 0.001 HIS L 6 PHE 0.013 0.001 PHE B 55 TYR 0.016 0.001 TYR A 56 ARG 0.009 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 124 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7674 (ttt) REVERT: B 105 HIS cc_start: 0.5125 (OUTLIER) cc_final: 0.4515 (m90) REVERT: B 107 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.6225 (UNCLASSIFIED) REVERT: B 237 GLN cc_start: 0.7226 (mt0) cc_final: 0.6895 (tt0) REVERT: B 303 GLN cc_start: 0.7364 (tm-30) cc_final: 0.7030 (tm-30) REVERT: B 333 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7618 (t0) REVERT: C 138 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8227 (mm-30) REVERT: C 186 ASP cc_start: 0.8721 (m-30) cc_final: 0.8513 (m-30) REVERT: C 247 ASP cc_start: 0.7963 (m-30) cc_final: 0.7427 (m-30) REVERT: C 258 ASP cc_start: 0.8351 (t0) cc_final: 0.7527 (t0) REVERT: C 325 MET cc_start: 0.8936 (mmt) cc_final: 0.8722 (tpp) outliers start: 29 outliers final: 19 residues processed: 111 average time/residue: 1.2880 time to fit residues: 152.5788 Evaluate side-chains 115 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 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 101 MET 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: 1.9990 chunk 26 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.172630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115304 restraints weight = 9528.146| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.80 r_work: 0.3089 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8896 Z= 0.227 Angle : 0.547 7.568 12086 Z= 0.286 Chirality : 0.043 0.151 1385 Planarity : 0.004 0.045 1495 Dihedral : 6.176 53.994 1583 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.34 % Allowed : 16.06 % Favored : 80.60 % 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: 0.88 (0.26), residues: 1050 helix: 1.97 (0.24), residues: 488 sheet: 0.37 (0.38), residues: 192 loop : -1.21 (0.31), residues: 370 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 C 199 TYR 0.012 0.001 TYR A 92 ARG 0.007 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 124 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.7901 (ttt) cc_final: 0.7656 (ttt) REVERT: B 105 HIS cc_start: 0.5103 (OUTLIER) cc_final: 0.4810 (m90) REVERT: B 237 GLN cc_start: 0.7250 (mt0) cc_final: 0.6941 (tt0) REVERT: B 299 GLN cc_start: 0.7724 (tt0) cc_final: 0.7187 (tp40) REVERT: B 303 GLN cc_start: 0.7152 (tm-30) cc_final: 0.6730 (tm-30) REVERT: B 321 ASP cc_start: 0.7212 (t0) cc_final: 0.6995 (t0) REVERT: C 138 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8056 (mm-30) REVERT: C 247 ASP cc_start: 0.7873 (m-30) cc_final: 0.7481 (m-30) REVERT: C 258 ASP cc_start: 0.8259 (t0) cc_final: 0.7471 (t0) outliers start: 31 outliers final: 23 residues processed: 112 average time/residue: 1.2810 time to fit residues: 152.9146 Evaluate side-chains 117 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 17 GLN Chi-restraints excluded: chain C residue 47 THR 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 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: 0.3980 chunk 101 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.175432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114095 restraints weight = 9485.272| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.53 r_work: 0.3181 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8896 Z= 0.153 Angle : 0.503 7.205 12086 Z= 0.263 Chirality : 0.041 0.135 1385 Planarity : 0.004 0.044 1495 Dihedral : 5.815 53.511 1579 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.69 % Allowed : 16.70 % Favored : 80.60 % 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: 1.07 (0.27), residues: 1050 helix: 2.18 (0.24), residues: 483 sheet: 0.49 (0.38), residues: 190 loop : -1.15 (0.31), residues: 377 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 0.013 0.001 PHE B 55 TYR 0.018 0.001 TYR A 56 ARG 0.012 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 123 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.7878 (ttt) cc_final: 0.7505 (ttt) REVERT: B 105 HIS cc_start: 0.5112 (OUTLIER) cc_final: 0.4850 (m90) REVERT: B 237 GLN cc_start: 0.7280 (mt0) cc_final: 0.6928 (tt0) REVERT: B 299 GLN cc_start: 0.7484 (tt0) cc_final: 0.6976 (tp40) REVERT: B 303 GLN cc_start: 0.7200 (tm-30) cc_final: 0.6869 (tm-30) REVERT: B 321 ASP cc_start: 0.7301 (t0) cc_final: 0.7061 (t0) REVERT: B 333 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7589 (t0) REVERT: C 138 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8202 (mm-30) REVERT: C 186 ASP cc_start: 0.8641 (m-30) cc_final: 0.8437 (m-30) REVERT: C 247 ASP cc_start: 0.7940 (m-30) cc_final: 0.7410 (m-30) REVERT: C 258 ASP cc_start: 0.8376 (t0) cc_final: 0.7473 (t0) outliers start: 25 outliers final: 20 residues processed: 112 average time/residue: 1.3054 time to fit residues: 156.1396 Evaluate side-chains 117 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 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 101 MET 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 71 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 52 optimal weight: 0.0000 chunk 64 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.175408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118899 restraints weight = 9469.804| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.73 r_work: 0.3130 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8896 Z= 0.165 Angle : 0.516 7.869 12086 Z= 0.269 Chirality : 0.041 0.141 1385 Planarity : 0.004 0.044 1495 Dihedral : 5.767 53.497 1579 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.48 % Allowed : 17.24 % 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: 1.11 (0.27), residues: 1050 helix: 2.21 (0.24), residues: 482 sheet: 0.52 (0.38), residues: 190 loop : -1.14 (0.31), residues: 378 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 0.014 0.001 PHE A 28 TYR 0.013 0.001 TYR B 356 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: 6355.50 seconds wall clock time: 112 minutes 52.60 seconds (6772.60 seconds total)