Starting phenix.real_space_refine on Thu Jul 2 15:36:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ykd_33891/07_2026/7ykd_33891.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ykd_33891/07_2026/7ykd_33891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ykd_33891/07_2026/7ykd_33891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ykd_33891/07_2026/7ykd_33891.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ykd_33891/07_2026/7ykd_33891.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ykd_33891/07_2026/7ykd_33891.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ykd_33891/07_2026/7ykd_33891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ykd_33891/07_2026/7ykd_33891.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.021 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 68 5.16 5 C 5778 2.51 5 N 1496 2.21 5 O 1623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8965 Number of models: 1 Model: "" Number of chains: 7 Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "A" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2250 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 10, 'TRANS': 271} Chain breaks: 1 Chain: "C" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1716 Classifications: {'peptide': 216} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2580 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 1.95, per 1000 atoms: 0.22 Number of scatterers: 8965 At special positions: 0 Unit cell: (87.98, 121.18, 121.18, 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 68 16.00 O 1623 8.00 N 1496 7.00 C 5778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 441.3 milliseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 38.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 35 through 68 Processing helix chain 'A' and resid 72 through 101 removed outlier: 3.675A pdb=" N TRP A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 108 through 143 removed outlier: 3.987A pdb=" N LEU A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'A' and resid 152 through 172 Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.680A pdb=" N VAL A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 177' Processing helix chain 'A' and resid 211 through 250 removed outlier: 6.143A pdb=" N VAL A 231 " --> pdb=" O CYS A 227 " (cutoff:3.500A) Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 256 through 283 Proline residue: A 275 - end of helix Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 290 through 317 removed outlier: 4.018A pdb=" N PHE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Proline residue: A 299 - end of helix Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 319 through 328 removed outlier: 3.975A pdb=" N PHE A 323 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.568A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 279 removed outlier: 4.200A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.610A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 removed outlier: 4.193A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 352 removed outlier: 3.651A pdb=" N GLN C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.656A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 183 removed outlier: 3.721A pdb=" N LEU A 183 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 191 removed outlier: 3.639A pdb=" N PHE C 189 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.141A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.511A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.968A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.752A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.651A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.635A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.010A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.654A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.340A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.577A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.661A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1438 1.32 - 1.44: 2502 1.44 - 1.56: 5131 1.56 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 9170 Sorted by residual: bond pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 1.523 1.442 0.081 1.34e-02 5.57e+03 3.68e+01 bond pdb=" CA LYS B 337 " pdb=" C LYS B 337 " ideal model delta sigma weight residual 1.521 1.471 0.050 1.24e-02 6.50e+03 1.61e+01 bond pdb=" C LEU A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 1.336 1.381 -0.045 1.23e-02 6.61e+03 1.36e+01 bond pdb=" CA PHE B 335 " pdb=" C PHE B 335 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.20e-02 6.94e+03 1.30e+01 bond pdb=" C LYS B 337 " pdb=" O LYS B 337 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.22e-02 6.72e+03 1.02e+01 ... (remaining 9165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 11910 1.85 - 3.71: 438 3.71 - 5.56: 75 5.56 - 7.41: 19 7.41 - 9.27: 7 Bond angle restraints: 12449 Sorted by residual: angle pdb=" N VAL S 2 " pdb=" CA VAL S 2 " pdb=" C VAL S 2 " ideal model delta sigma weight residual 112.43 104.83 7.60 9.20e-01 1.18e+00 6.82e+01 angle pdb=" N LEU B 336 " pdb=" CA LEU B 336 " pdb=" C LEU B 336 " ideal model delta sigma weight residual 109.40 102.00 7.40 1.63e+00 3.76e-01 2.06e+01 angle pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" O ASP B 291 " ideal model delta sigma weight residual 120.51 114.44 6.07 1.43e+00 4.89e-01 1.80e+01 angle pdb=" N VAL A 141 " pdb=" CA VAL A 141 " pdb=" C VAL A 141 " ideal model delta sigma weight residual 111.90 108.60 3.30 8.10e-01 1.52e+00 1.66e+01 angle pdb=" CA LEU A 143 " pdb=" C LEU A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 117.73 121.77 -4.04 1.04e+00 9.25e-01 1.51e+01 ... (remaining 12444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.97: 5137 23.97 - 47.94: 203 47.94 - 71.91: 29 71.91 - 95.88: 2 95.88 - 119.85: 1 Dihedral angle restraints: 5372 sinusoidal: 2093 harmonic: 3279 Sorted by residual: dihedral pdb=" CB CYS A 112 " pdb=" SG CYS A 112 " pdb=" SG CYS A 189 " pdb=" CB CYS A 189 " ideal model delta sinusoidal sigma weight residual 93.00 161.98 -68.98 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 152.46 27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA PHE A 67 " pdb=" C PHE A 67 " pdb=" N LYS A 68 " pdb=" CA LYS A 68 " ideal model delta harmonic sigma weight residual -180.00 -158.32 -21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1218 0.075 - 0.150: 204 0.150 - 0.226: 5 0.226 - 0.301: 3 0.301 - 0.376: 3 Chirality restraints: 1433 Sorted by residual: chirality pdb=" CA ASP B 312 " pdb=" N ASP B 312 " pdb=" C ASP B 312 " pdb=" CB ASP B 312 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C20 CLR A 403 " pdb=" C17 CLR A 403 " pdb=" C21 CLR A 403 " pdb=" C22 CLR A 403 " both_signs ideal model delta sigma weight residual False 2.59 2.23 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C20 CLR A 405 " pdb=" C17 CLR A 405 " pdb=" C21 CLR A 405 " pdb=" C22 CLR A 405 " both_signs ideal model delta sigma weight residual False 2.59 2.24 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 1430 not shown) Planarity restraints: 1535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 23 " 0.033 2.00e-02 2.50e+03 2.02e-02 7.16e+00 pdb=" CG PHE L 23 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE L 23 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE L 23 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE L 23 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE L 23 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE L 23 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO S 75 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 226 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C LEU A 226 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU A 226 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS A 227 " -0.011 2.00e-02 2.50e+03 ... (remaining 1532 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 202 2.67 - 3.23: 8639 3.23 - 3.79: 14242 3.79 - 4.34: 19809 4.34 - 4.90: 33702 Nonbonded interactions: 76594 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.118 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.122 3.040 nonbonded pdb=" C25 CLR A 402 " pdb=" C21 CLR A 403 " model vdw 2.146 3.890 nonbonded pdb=" NZ LYS S 244 " pdb=" OE2 GLU S 246 " model vdw 2.160 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.175 3.120 ... (remaining 76589 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: 2.710 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.430 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.012 0.753 9174 Z= 0.877 Angle : 0.863 9.265 12455 Z= 0.462 Chirality : 0.055 0.376 1433 Planarity : 0.004 0.057 1535 Dihedral : 13.077 119.850 3245 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.10 % Allowed : 0.83 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.25), residues: 1111 helix: 0.91 (0.26), residues: 382 sheet: -0.04 (0.32), residues: 288 loop : -1.01 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 24 TYR 0.019 0.002 TYR B 105 PHE 0.033 0.003 PHE L 23 TRP 0.018 0.002 TRP S 47 HIS 0.006 0.002 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00870 / 0.39 ( 9170) covalent geometry : angle 0.85964 / 0.46 (12449) SS BOND : bond 0.00381 / 0.19 ( 3) SS BOND : angle 3.50994 / 1.95 ( 6) hydrogen bonds : bond 0.16320 / 10.50 ( 465) hydrogen bonds : angle 6.98139 / 5.09 ( 1308) Misc. bond : bond 0.75319 / 39.64 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.409 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 33 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7468 (mm-30) REVERT: B 291 ASP cc_start: 0.7436 (m-30) cc_final: 0.7077 (m-30) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.6396 time to fit residues: 100.7195 Evaluate side-chains 118 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.146768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102047 restraints weight = 11600.789| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.39 r_work: 0.3127 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9174 Z= 0.162 Angle : 0.666 8.519 12455 Z= 0.336 Chirality : 0.046 0.317 1433 Planarity : 0.004 0.049 1535 Dihedral : 7.386 116.400 1259 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.88 % Allowed : 9.17 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.25), residues: 1111 helix: 1.55 (0.26), residues: 386 sheet: 0.04 (0.32), residues: 263 loop : -0.89 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.016 0.001 TYR B 59 PHE 0.016 0.001 PHE A 190 TRP 0.018 0.002 TRP B 82 HIS 0.008 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 9170) covalent geometry : angle 0.66567 / 0.34 (12449) SS BOND : bond 0.00391 / 0.19 ( 3) SS BOND : angle 1.38068 / 0.85 ( 6) hydrogen bonds : bond 0.04305 / 2.77 ( 465) hydrogen bonds : angle 5.09174 / 3.72 ( 1308) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.298 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 33 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7461 (mm-30) REVERT: C 248 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7552 (mmtt) REVERT: B 13 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8498 (pp30) REVERT: B 19 ARG cc_start: 0.7598 (tmm160) cc_final: 0.7348 (ttp-110) REVERT: B 23 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8354 (ttmt) REVERT: B 198 LEU cc_start: 0.8240 (pp) cc_final: 0.8009 (pt) REVERT: S 18 ARG cc_start: 0.8550 (tpp80) cc_final: 0.8347 (tpp80) REVERT: S 202 ARG cc_start: 0.8021 (ptt-90) cc_final: 0.7752 (ptt-90) outliers start: 18 outliers final: 7 residues processed: 133 average time/residue: 0.5494 time to fit residues: 77.6409 Evaluate side-chains 122 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 107 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 71 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN B 75 GLN S 82 GLN S 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100195 restraints weight = 11592.894| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.61 r_work: 0.3118 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9174 Z= 0.143 Angle : 0.618 13.561 12455 Z= 0.309 Chirality : 0.044 0.257 1433 Planarity : 0.004 0.045 1535 Dihedral : 7.359 114.821 1259 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.67 % Allowed : 12.08 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1111 helix: 1.88 (0.26), residues: 385 sheet: -0.08 (0.31), residues: 267 loop : -0.84 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.014 0.001 TYR B 59 PHE 0.011 0.001 PHE C 274 TRP 0.017 0.001 TRP B 82 HIS 0.010 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9170) covalent geometry : angle 0.61790 / 0.31 (12449) SS BOND : bond 0.00322 / 0.16 ( 3) SS BOND : angle 0.89131 / 0.59 ( 6) hydrogen bonds : bond 0.03750 / 2.40 ( 465) hydrogen bonds : angle 4.75385 / 3.48 ( 1308) Misc. bond : bond 0.00086 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.331 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6532 (tt0) REVERT: C 33 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7502 (mm-30) REVERT: C 248 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7361 (mmtt) REVERT: C 263 SER cc_start: 0.9022 (m) cc_final: 0.8732 (p) REVERT: B 19 ARG cc_start: 0.7475 (tmm160) cc_final: 0.7228 (ttp-110) REVERT: B 44 GLN cc_start: 0.8434 (mt0) cc_final: 0.7989 (mm-40) REVERT: B 160 SER cc_start: 0.8519 (t) cc_final: 0.7746 (p) REVERT: B 215 GLU cc_start: 0.8432 (mp0) cc_final: 0.8201 (OUTLIER) REVERT: S 18 ARG cc_start: 0.8328 (tpp80) cc_final: 0.8086 (tpp80) REVERT: S 202 ARG cc_start: 0.7741 (ptt-90) cc_final: 0.7460 (ptt-90) REVERT: S 246 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8105 (mt-10) outliers start: 16 outliers final: 4 residues processed: 140 average time/residue: 0.5909 time to fit residues: 87.7308 Evaluate side-chains 127 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN C 256 ASN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100548 restraints weight = 11703.252| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.63 r_work: 0.3111 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9174 Z= 0.142 Angle : 0.610 13.749 12455 Z= 0.304 Chirality : 0.044 0.250 1433 Planarity : 0.004 0.044 1535 Dihedral : 7.322 115.139 1259 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.08 % Allowed : 14.06 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1111 helix: 2.02 (0.26), residues: 385 sheet: -0.08 (0.31), residues: 264 loop : -0.82 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.013 0.001 TYR B 264 PHE 0.014 0.001 PHE A 52 TRP 0.016 0.001 TRP B 82 HIS 0.010 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9170) covalent geometry : angle 0.60972 / 0.30 (12449) SS BOND : bond 0.00359 / 0.18 ( 3) SS BOND : angle 1.02378 / 0.65 ( 6) hydrogen bonds : bond 0.03601 / 2.30 ( 465) hydrogen bonds : angle 4.66713 / 3.42 ( 1308) Misc. bond : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.362 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6524 (tt0) REVERT: C 33 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7524 (mt-10) REVERT: C 248 LYS cc_start: 0.7697 (mmtt) cc_final: 0.7430 (mmtt) REVERT: B 19 ARG cc_start: 0.7587 (tmm160) cc_final: 0.7287 (ttp-110) REVERT: B 44 GLN cc_start: 0.8441 (mt0) cc_final: 0.8028 (mm-40) REVERT: B 100 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8700 (m) REVERT: B 197 ARG cc_start: 0.7852 (mmp-170) cc_final: 0.7652 (mtp85) REVERT: B 217 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7209 (pmm) REVERT: G 42 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: S 18 ARG cc_start: 0.8346 (tpp80) cc_final: 0.8066 (tpp80) REVERT: S 186 GLN cc_start: 0.8245 (tt0) cc_final: 0.8023 (pt0) REVERT: S 202 ARG cc_start: 0.7755 (ptt-90) cc_final: 0.7413 (ptt-90) REVERT: S 246 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8046 (mt-10) outliers start: 20 outliers final: 9 residues processed: 136 average time/residue: 0.6047 time to fit residues: 87.5171 Evaluate side-chains 130 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 43 optimal weight: 0.0010 chunk 94 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 106 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.147191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101677 restraints weight = 11572.145| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.63 r_work: 0.3126 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9174 Z= 0.128 Angle : 0.599 15.067 12455 Z= 0.299 Chirality : 0.044 0.250 1433 Planarity : 0.004 0.043 1535 Dihedral : 7.243 113.041 1259 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.29 % Allowed : 15.00 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.26), residues: 1111 helix: 2.16 (0.26), residues: 385 sheet: -0.12 (0.30), residues: 276 loop : -0.77 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 134 TYR 0.012 0.001 TYR B 264 PHE 0.010 0.001 PHE A 124 TRP 0.016 0.001 TRP B 82 HIS 0.010 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9170) covalent geometry : angle 0.59833 / 0.30 (12449) SS BOND : bond 0.00344 / 0.17 ( 3) SS BOND : angle 0.88346 / 0.56 ( 6) hydrogen bonds : bond 0.03453 / 2.20 ( 465) hydrogen bonds : angle 4.56209 / 3.35 ( 1308) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.374 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 289 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8410 (mtp) REVERT: C 25 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6515 (tt0) REVERT: C 33 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7462 (mt-10) REVERT: C 53 MET cc_start: 0.6563 (mpp) cc_final: 0.6275 (mtt) REVERT: C 248 LYS cc_start: 0.7678 (mmtt) cc_final: 0.7442 (mmtt) REVERT: C 263 SER cc_start: 0.9039 (m) cc_final: 0.8758 (p) REVERT: B 19 ARG cc_start: 0.7617 (tmm160) cc_final: 0.7182 (ttp-110) REVERT: B 44 GLN cc_start: 0.8461 (mt0) cc_final: 0.8055 (mm-40) REVERT: B 100 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8692 (m) REVERT: B 135 VAL cc_start: 0.8947 (t) cc_final: 0.8702 (p) REVERT: B 197 ARG cc_start: 0.7864 (mmp-170) cc_final: 0.7470 (mtp85) REVERT: B 217 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7126 (pmm) REVERT: B 274 THR cc_start: 0.8797 (p) cc_final: 0.8513 (p) REVERT: B 301 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7878 (mtpp) REVERT: G 21 MET cc_start: 0.8322 (tpp) cc_final: 0.8035 (tpp) REVERT: G 42 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: S 18 ARG cc_start: 0.8350 (tpp80) cc_final: 0.8093 (tpp80) REVERT: S 186 GLN cc_start: 0.8261 (tt0) cc_final: 0.7918 (pt0) REVERT: S 202 ARG cc_start: 0.7812 (ptt-90) cc_final: 0.7435 (ptt-90) REVERT: S 246 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8006 (mt-10) outliers start: 22 outliers final: 7 residues processed: 143 average time/residue: 0.6161 time to fit residues: 93.7074 Evaluate side-chains 133 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.145574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099894 restraints weight = 11695.991| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.63 r_work: 0.3099 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9174 Z= 0.166 Angle : 0.632 15.853 12455 Z= 0.313 Chirality : 0.045 0.245 1433 Planarity : 0.004 0.044 1535 Dihedral : 7.324 112.836 1259 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.92 % Allowed : 15.73 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.26), residues: 1111 helix: 2.13 (0.26), residues: 385 sheet: -0.14 (0.30), residues: 278 loop : -0.74 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.015 0.001 TYR B 264 PHE 0.016 0.001 PHE A 52 TRP 0.013 0.001 TRP A 77 HIS 0.010 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 9170) covalent geometry : angle 0.63206 / 0.31 (12449) SS BOND : bond 0.00382 / 0.19 ( 3) SS BOND : angle 0.91526 / 0.58 ( 6) hydrogen bonds : bond 0.03642 / 2.32 ( 465) hydrogen bonds : angle 4.59767 / 3.38 ( 1308) Misc. bond : bond 0.00095 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.372 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6540 (tt0) REVERT: C 33 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7515 (mt-10) REVERT: C 53 MET cc_start: 0.6590 (mpp) cc_final: 0.6328 (mtt) REVERT: C 248 LYS cc_start: 0.7716 (mmtt) cc_final: 0.7467 (mmtt) REVERT: B 19 ARG cc_start: 0.7655 (tmm160) cc_final: 0.7201 (ttp-110) REVERT: B 44 GLN cc_start: 0.8458 (mt0) cc_final: 0.8059 (mm-40) REVERT: B 100 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8722 (m) REVERT: B 198 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7796 (pt) REVERT: B 217 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7125 (pmm) REVERT: B 301 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7951 (mtpp) REVERT: G 21 MET cc_start: 0.8351 (tpp) cc_final: 0.8062 (tpp) REVERT: G 42 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: S 18 ARG cc_start: 0.8375 (tpp80) cc_final: 0.8102 (tpp80) REVERT: S 202 ARG cc_start: 0.7789 (ptt-90) cc_final: 0.7399 (ptt-90) REVERT: S 246 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8134 (mt-10) outliers start: 28 outliers final: 11 residues processed: 138 average time/residue: 0.6415 time to fit residues: 93.8700 Evaluate side-chains 133 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 110 optimal weight: 0.0000 chunk 109 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.147004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.101424 restraints weight = 11721.467| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.61 r_work: 0.3132 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9174 Z= 0.135 Angle : 0.616 16.509 12455 Z= 0.305 Chirality : 0.044 0.247 1433 Planarity : 0.004 0.043 1535 Dihedral : 7.310 114.020 1259 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.60 % Allowed : 16.98 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.26), residues: 1111 helix: 2.18 (0.26), residues: 385 sheet: -0.06 (0.29), residues: 287 loop : -0.74 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 134 TYR 0.012 0.001 TYR B 264 PHE 0.011 0.001 PHE B 151 TRP 0.014 0.001 TRP A 77 HIS 0.010 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 9170) covalent geometry : angle 0.61556 / 0.31 (12449) SS BOND : bond 0.00359 / 0.18 ( 3) SS BOND : angle 0.85472 / 0.53 ( 6) hydrogen bonds : bond 0.03440 / 2.17 ( 465) hydrogen bonds : angle 4.52510 / 3.32 ( 1308) Misc. bond : bond 0.00062 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.255 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6511 (tt0) REVERT: C 33 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7492 (mt-10) REVERT: C 53 MET cc_start: 0.6618 (mpp) cc_final: 0.6347 (mtt) REVERT: C 248 LYS cc_start: 0.7690 (mmtt) cc_final: 0.7447 (mmtt) REVERT: C 263 SER cc_start: 0.9042 (m) cc_final: 0.8758 (p) REVERT: B 19 ARG cc_start: 0.7616 (tmm160) cc_final: 0.7159 (ttp-110) REVERT: B 44 GLN cc_start: 0.8454 (mt0) cc_final: 0.8056 (mm-40) REVERT: B 100 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8659 (m) REVERT: B 135 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8726 (p) REVERT: B 198 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7799 (pt) REVERT: B 217 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7177 (pmm) REVERT: B 274 THR cc_start: 0.8745 (p) cc_final: 0.8476 (p) REVERT: B 301 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7951 (mtpp) REVERT: G 21 MET cc_start: 0.8343 (tpp) cc_final: 0.8052 (tpp) REVERT: G 42 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: S 18 ARG cc_start: 0.8361 (tpp80) cc_final: 0.8076 (tpp80) REVERT: S 186 GLN cc_start: 0.8259 (tt0) cc_final: 0.7841 (pt0) REVERT: S 202 ARG cc_start: 0.7758 (ptt-90) cc_final: 0.7370 (ptt-90) REVERT: S 246 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8093 (mt-10) outliers start: 25 outliers final: 12 residues processed: 135 average time/residue: 0.6259 time to fit residues: 89.6956 Evaluate side-chains 133 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 101 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102632 restraints weight = 11655.552| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.61 r_work: 0.3152 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9174 Z= 0.124 Angle : 0.610 17.180 12455 Z= 0.301 Chirality : 0.043 0.246 1433 Planarity : 0.004 0.043 1535 Dihedral : 7.275 114.597 1259 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.40 % Allowed : 17.60 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1111 helix: 2.27 (0.26), residues: 385 sheet: -0.04 (0.29), residues: 287 loop : -0.70 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 134 TYR 0.012 0.001 TYR B 264 PHE 0.020 0.001 PHE A 52 TRP 0.015 0.001 TRP B 82 HIS 0.010 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 9170) covalent geometry : angle 0.60948 / 0.30 (12449) SS BOND : bond 0.00344 / 0.17 ( 3) SS BOND : angle 0.89391 / 0.54 ( 6) hydrogen bonds : bond 0.03341 / 2.10 ( 465) hydrogen bonds : angle 4.46520 / 3.28 ( 1308) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.351 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 321 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6912 (mm-40) REVERT: C 25 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6472 (tt0) REVERT: C 33 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7433 (mt-10) REVERT: C 53 MET cc_start: 0.6553 (mpp) cc_final: 0.6298 (mtt) REVERT: C 248 LYS cc_start: 0.7659 (mmtt) cc_final: 0.7426 (mmtt) REVERT: C 263 SER cc_start: 0.9026 (m) cc_final: 0.8748 (p) REVERT: B 19 ARG cc_start: 0.7585 (tmm160) cc_final: 0.7134 (ttp-110) REVERT: B 44 GLN cc_start: 0.8426 (mt0) cc_final: 0.8049 (mm-40) REVERT: B 100 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8479 (m) REVERT: B 135 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8673 (p) REVERT: B 198 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7568 (pp) REVERT: B 217 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7176 (pmm) REVERT: B 274 THR cc_start: 0.8720 (p) cc_final: 0.8437 (p) REVERT: B 301 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7875 (mtpp) REVERT: G 21 MET cc_start: 0.8331 (tpp) cc_final: 0.8044 (tpp) REVERT: G 42 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: S 18 ARG cc_start: 0.8345 (tpp80) cc_final: 0.8060 (tpp80) REVERT: S 46 GLU cc_start: 0.7843 (tt0) cc_final: 0.7168 (pt0) REVERT: S 186 GLN cc_start: 0.8236 (tt0) cc_final: 0.7804 (pt0) REVERT: S 246 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8064 (mt-10) outliers start: 23 outliers final: 10 residues processed: 137 average time/residue: 0.6297 time to fit residues: 91.6060 Evaluate side-chains 132 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101067 restraints weight = 11609.230| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.63 r_work: 0.3119 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9174 Z= 0.155 Angle : 0.639 17.724 12455 Z= 0.316 Chirality : 0.044 0.240 1433 Planarity : 0.004 0.043 1535 Dihedral : 7.326 113.767 1259 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.29 % Allowed : 18.44 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.26), residues: 1111 helix: 2.23 (0.26), residues: 385 sheet: -0.10 (0.29), residues: 277 loop : -0.67 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.011 0.001 TYR B 264 PHE 0.011 0.001 PHE A 124 TRP 0.014 0.001 TRP A 77 HIS 0.010 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 9170) covalent geometry : angle 0.63855 / 0.32 (12449) SS BOND : bond 0.00364 / 0.18 ( 3) SS BOND : angle 0.91765 / 0.54 ( 6) hydrogen bonds : bond 0.03528 / 2.23 ( 465) hydrogen bonds : angle 4.51601 / 3.32 ( 1308) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.360 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 69 MET cc_start: 0.5250 (mtt) cc_final: 0.5006 (mtt) REVERT: C 25 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6515 (tt0) REVERT: C 33 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7522 (mt-10) REVERT: C 248 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7434 (mmtt) REVERT: C 263 SER cc_start: 0.9039 (m) cc_final: 0.8753 (p) REVERT: B 19 ARG cc_start: 0.7632 (tmm160) cc_final: 0.7194 (ttp-110) REVERT: B 44 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8084 (mm-40) REVERT: B 135 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8709 (p) REVERT: B 198 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7619 (pp) REVERT: B 217 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.7214 (pmm) REVERT: B 274 THR cc_start: 0.8807 (p) cc_final: 0.8529 (p) REVERT: B 301 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7944 (mtpp) REVERT: G 21 MET cc_start: 0.8328 (tpp) cc_final: 0.8035 (tpp) REVERT: G 42 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: S 18 ARG cc_start: 0.8362 (tpp80) cc_final: 0.8074 (tpp80) REVERT: S 186 GLN cc_start: 0.8270 (tt0) cc_final: 0.7944 (pt0) REVERT: S 246 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8081 (mt-10) outliers start: 22 outliers final: 9 residues processed: 133 average time/residue: 0.6739 time to fit residues: 94.9582 Evaluate side-chains 130 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 0.0070 chunk 1 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 94 optimal weight: 0.0370 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN C 256 ASN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.149070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.104507 restraints weight = 11480.660| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.57 r_work: 0.3163 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9174 Z= 0.118 Angle : 0.634 17.821 12455 Z= 0.313 Chirality : 0.043 0.242 1433 Planarity : 0.004 0.047 1535 Dihedral : 7.280 114.990 1259 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.67 % Allowed : 19.38 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.26), residues: 1111 helix: 2.27 (0.26), residues: 386 sheet: 0.06 (0.30), residues: 284 loop : -0.69 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 134 TYR 0.011 0.001 TYR B 59 PHE 0.022 0.001 PHE A 52 TRP 0.015 0.001 TRP A 77 HIS 0.010 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9170) covalent geometry : angle 0.63411 / 0.31 (12449) SS BOND : bond 0.00272 / 0.14 ( 3) SS BOND : angle 0.95210 / 0.57 ( 6) hydrogen bonds : bond 0.03235 / 2.03 ( 465) hydrogen bonds : angle 4.42333 / 3.25 ( 1308) Misc. bond : bond 0.00044 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.353 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 191 ASN cc_start: 0.7116 (OUTLIER) cc_final: 0.6594 (t0) REVERT: C 25 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6577 (tt0) REVERT: C 33 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7478 (mt-10) REVERT: C 248 LYS cc_start: 0.7617 (mmtt) cc_final: 0.7380 (mmtt) REVERT: C 263 SER cc_start: 0.9054 (m) cc_final: 0.8792 (p) REVERT: B 19 ARG cc_start: 0.7602 (tmm160) cc_final: 0.7139 (ttp-110) REVERT: B 44 GLN cc_start: 0.8448 (mt0) cc_final: 0.8085 (mm-40) REVERT: B 135 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8665 (p) REVERT: B 198 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7600 (pp) REVERT: B 217 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7224 (pmm) REVERT: B 274 THR cc_start: 0.8721 (p) cc_final: 0.8437 (p) REVERT: B 301 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7932 (mtpp) REVERT: G 21 MET cc_start: 0.8329 (tpp) cc_final: 0.8033 (tpp) REVERT: G 42 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: S 18 ARG cc_start: 0.8363 (tpp80) cc_final: 0.8083 (tpp80) REVERT: S 46 GLU cc_start: 0.7851 (tt0) cc_final: 0.7223 (pt0) REVERT: S 186 GLN cc_start: 0.8276 (tt0) cc_final: 0.7989 (pt0) REVERT: S 246 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8051 (mt-10) outliers start: 16 outliers final: 7 residues processed: 134 average time/residue: 0.6076 time to fit residues: 86.5707 Evaluate side-chains 127 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 103 optimal weight: 0.0770 chunk 46 optimal weight: 4.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.148553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103752 restraints weight = 11392.778| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.56 r_work: 0.3153 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9174 Z= 0.136 Angle : 0.648 17.524 12455 Z= 0.322 Chirality : 0.045 0.356 1433 Planarity : 0.004 0.046 1535 Dihedral : 7.314 114.749 1259 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.25 % Allowed : 19.38 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.26), residues: 1111 helix: 2.23 (0.26), residues: 387 sheet: -0.01 (0.30), residues: 286 loop : -0.66 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 134 TYR 0.011 0.001 TYR B 59 PHE 0.030 0.001 PHE C 274 TRP 0.014 0.001 TRP A 77 HIS 0.009 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 9170) covalent geometry : angle 0.64731 / 0.32 (12449) SS BOND : bond 0.00284 / 0.14 ( 3) SS BOND : angle 1.10201 / 0.69 ( 6) hydrogen bonds : bond 0.03331 / 2.08 ( 465) hydrogen bonds : angle 4.43300 / 3.26 ( 1308) Misc. bond : bond 0.00052 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3697.83 seconds wall clock time: 63 minutes 51.36 seconds (3831.36 seconds total)