Starting phenix.real_space_refine on Fri Aug 22 17:16:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwh_27754/08_2025/8dwh_27754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwh_27754/08_2025/8dwh_27754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dwh_27754/08_2025/8dwh_27754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwh_27754/08_2025/8dwh_27754.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dwh_27754/08_2025/8dwh_27754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwh_27754/08_2025/8dwh_27754.map" } resolution = 3.25 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= 0.023 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 44 5.16 5 C 4136 2.51 5 N 1103 2.21 5 O 1161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6444 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1704 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2480 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 92 Chain: "D" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1879 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 241} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'PHE:plan': 2, 'HIS:plan': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'U2U': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.94, per 1000 atoms: 0.30 Number of scatterers: 6444 At special positions: 0 Unit cell: (90.64, 101.2, 121.44, 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 44 16.00 O 1161 8.00 N 1103 7.00 C 4136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 161 " - pdb=" SG CYS R 173 " 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 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 364.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 9 sheets defined 46.3% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.597A pdb=" N LYS B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.627A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP B 102 " --> pdb=" O CYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 132 through 135 removed outlier: 3.663A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.517A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 170 removed outlier: 3.756A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 204 removed outlier: 3.710A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 Processing helix chain 'C' and resid 4 through 23 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'R' and resid 26 through 55 removed outlier: 4.027A pdb=" N GLY R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS R 54 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 88 removed outlier: 3.546A pdb=" N ILE R 63 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE R 87 " --> pdb=" O SER R 83 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE R 88 " --> pdb=" O LEU R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 126 removed outlier: 3.865A pdb=" N TYR R 99 " --> pdb=" O SER R 95 " (cutoff:3.500A) Proline residue: R 100 - end of helix removed outlier: 4.927A pdb=" N PHE R 104 " --> pdb=" O PRO R 100 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 132 Processing helix chain 'R' and resid 137 through 161 Processing helix chain 'R' and resid 172 through 204 removed outlier: 3.985A pdb=" N SER R 176 " --> pdb=" O TRP R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 229 removed outlier: 3.873A pdb=" N PHE R 225 " --> pdb=" O THR R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 235 removed outlier: 3.661A pdb=" N ILE R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 242 Processing helix chain 'R' and resid 245 through 252 removed outlier: 4.125A pdb=" N PHE R 250 " --> pdb=" O ARG R 246 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N CYS R 251 " --> pdb=" O GLU R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 273 removed outlier: 3.524A pdb=" N SER R 265 " --> pdb=" O SER R 261 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER R 266 " --> pdb=" O ALA R 262 " (cutoff:3.500A) Proline residue: R 269 - end of helix Processing helix chain 'R' and resid 274 through 278 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.341A pdb=" N LEU B 34 " --> pdb=" O HIS B 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.214A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.891A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 328 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C 318 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY C 330 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.769A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.965A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.595A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.762A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.603A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.950A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 978 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: 1.07 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2079 1.34 - 1.46: 1452 1.46 - 1.58: 2990 1.58 - 1.69: 1 1.69 - 1.81: 56 Bond restraints: 6578 Sorted by residual: bond pdb=" C22 U2U R 401 " pdb=" N3 U2U R 401 " ideal model delta sigma weight residual 1.370 1.341 0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" CB PRO D 60 " pdb=" CG PRO D 60 " ideal model delta sigma weight residual 1.492 1.553 -0.061 5.00e-02 4.00e+02 1.51e+00 bond pdb=" CG LEU R 191 " pdb=" CD2 LEU R 191 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" C21 U2U R 401 " pdb=" N2 U2U R 401 " ideal model delta sigma weight residual 1.359 1.339 0.020 2.00e-02 2.50e+03 9.93e-01 bond pdb=" CA ASP B 85 " pdb=" CB ASP B 85 " ideal model delta sigma weight residual 1.536 1.560 -0.024 2.53e-02 1.56e+03 8.92e-01 ... (remaining 6573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 8780 1.58 - 3.17: 148 3.17 - 4.75: 24 4.75 - 6.33: 10 6.33 - 7.91: 2 Bond angle restraints: 8964 Sorted by residual: angle pdb=" N ASP C 153 " pdb=" CA ASP C 153 " pdb=" C ASP C 153 " ideal model delta sigma weight residual 108.24 104.62 3.62 1.32e+00 5.74e-01 7.53e+00 angle pdb=" N GLY C 319 " pdb=" CA GLY C 319 " pdb=" C GLY C 319 " ideal model delta sigma weight residual 110.87 114.62 -3.75 1.54e+00 4.22e-01 5.91e+00 angle pdb=" CB ARG C 304 " pdb=" CG ARG C 304 " pdb=" CD ARG C 304 " ideal model delta sigma weight residual 111.30 106.02 5.28 2.30e+00 1.89e-01 5.27e+00 angle pdb=" CA LEU C 190 " pdb=" CB LEU C 190 " pdb=" CG LEU C 190 " ideal model delta sigma weight residual 116.30 124.21 -7.91 3.50e+00 8.16e-02 5.11e+00 angle pdb=" C ASP C 195 " pdb=" N THR C 196 " pdb=" CA THR C 196 " ideal model delta sigma weight residual 122.46 125.59 -3.13 1.41e+00 5.03e-01 4.94e+00 ... (remaining 8959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.96: 3374 13.96 - 27.92: 333 27.92 - 41.88: 103 41.88 - 55.83: 23 55.83 - 69.79: 2 Dihedral angle restraints: 3835 sinusoidal: 1340 harmonic: 2495 Sorted by residual: dihedral pdb=" CA PRO R 100 " pdb=" C PRO R 100 " pdb=" N VAL R 101 " pdb=" CA VAL R 101 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ASN B 223 " pdb=" CB ASN B 223 " pdb=" CG ASN B 223 " pdb=" OD1 ASN B 223 " ideal model delta sinusoidal sigma weight residual 120.00 -175.31 -64.69 2 2.00e+01 2.50e-03 9.81e+00 dihedral pdb=" CG ARG C 68 " pdb=" CD ARG C 68 " pdb=" NE ARG C 68 " pdb=" CZ ARG C 68 " ideal model delta sinusoidal sigma weight residual -90.00 -131.73 41.73 2 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 619 0.030 - 0.060: 296 0.060 - 0.090: 90 0.090 - 0.120: 46 0.120 - 0.150: 10 Chirality restraints: 1061 Sorted by residual: chirality pdb=" CA PRO R 231 " pdb=" N PRO R 231 " pdb=" C PRO R 231 " pdb=" CB PRO R 231 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CG LEU R 191 " pdb=" CB LEU R 191 " pdb=" CD1 LEU R 191 " pdb=" CD2 LEU R 191 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ASN B 43 " pdb=" N ASN B 43 " pdb=" C ASN B 43 " pdb=" CB ASN B 43 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1058 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 230 " 0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO R 231 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 231 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 231 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO C 236 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " 0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO D 49 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " 0.020 5.00e-02 4.00e+02 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 117 2.68 - 3.24: 6284 3.24 - 3.79: 9795 3.79 - 4.35: 13265 4.35 - 4.90: 22169 Nonbonded interactions: 51630 Sorted by model distance: nonbonded pdb=" OH TYR R 64 " pdb=" OE2 GLU R 119 " model vdw 2.129 3.040 nonbonded pdb=" OD1 ASP C 153 " pdb=" N ASP C 154 " model vdw 2.133 3.120 nonbonded pdb=" OH TYR B 243 " pdb=" OH TYR R 130 " model vdw 2.159 3.040 nonbonded pdb=" OE1 GLU B 182 " pdb=" OG1 THR B 187 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR R 106 " pdb=" O PHE R 232 " model vdw 2.216 3.040 ... (remaining 51625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.300 Find NCS groups from input model: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.004 0.061 6579 Z= 0.175 Angle : 0.567 7.913 8966 Z= 0.309 Chirality : 0.042 0.150 1061 Planarity : 0.003 0.052 1122 Dihedral : 12.917 69.793 2210 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.29), residues: 844 helix: 0.07 (0.28), residues: 356 sheet: -0.32 (0.45), residues: 145 loop : -1.41 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 15 TYR 0.009 0.001 TYR C 105 PHE 0.012 0.001 PHE C 199 TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6578) covalent geometry : angle 0.56682 ( 8964) SS BOND : bond 0.00180 ( 1) SS BOND : angle 0.90563 ( 2) hydrogen bonds : bond 0.25672 ( 344) hydrogen bonds : angle 8.23049 ( 978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.256 Fit side-chains REVERT: B 122 LEU cc_start: 0.7986 (mp) cc_final: 0.7733 (mp) REVERT: B 128 ILE cc_start: 0.8048 (mm) cc_final: 0.7847 (mt) REVERT: B 145 LYS cc_start: 0.8297 (mtpp) cc_final: 0.8001 (mtpt) REVERT: B 210 ILE cc_start: 0.8138 (mt) cc_final: 0.7906 (mt) REVERT: C 68 ARG cc_start: 0.8105 (ttt180) cc_final: 0.7497 (ttt-90) REVERT: C 134 ARG cc_start: 0.6814 (pmt-80) cc_final: 0.6428 (pmt-80) REVERT: C 258 ASP cc_start: 0.7135 (t70) cc_final: 0.6340 (t0) REVERT: C 285 LEU cc_start: 0.8462 (tt) cc_final: 0.8258 (tt) REVERT: R 65 ILE cc_start: 0.7733 (mm) cc_final: 0.7487 (mt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1136 time to fit residues: 23.1417 Evaluate side-chains 145 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.116211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.099943 restraints weight = 9466.783| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.19 r_work: 0.3092 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6579 Z= 0.189 Angle : 0.605 7.115 8966 Z= 0.313 Chirality : 0.044 0.137 1061 Planarity : 0.004 0.036 1122 Dihedral : 4.458 25.568 927 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.09 % Allowed : 8.40 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.30), residues: 844 helix: 1.31 (0.29), residues: 360 sheet: -0.28 (0.41), residues: 163 loop : -1.39 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 304 TYR 0.014 0.002 TYR C 59 PHE 0.012 0.001 PHE R 225 TRP 0.015 0.001 TRP C 82 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 6578) covalent geometry : angle 0.60445 ( 8964) SS BOND : bond 0.00217 ( 1) SS BOND : angle 0.87012 ( 2) hydrogen bonds : bond 0.05355 ( 344) hydrogen bonds : angle 4.88363 ( 978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 0.330 Fit side-chains REVERT: B 8 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6665 (tm-30) REVERT: B 122 LEU cc_start: 0.7986 (mp) cc_final: 0.7684 (mp) REVERT: C 68 ARG cc_start: 0.8374 (ttt180) cc_final: 0.7713 (ttt-90) REVERT: C 76 ASP cc_start: 0.7489 (p0) cc_final: 0.7244 (p0) REVERT: C 102 THR cc_start: 0.8250 (m) cc_final: 0.7952 (p) REVERT: C 134 ARG cc_start: 0.7173 (pmt-80) cc_final: 0.6753 (pmt-80) REVERT: C 219 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7690 (mtt180) REVERT: C 258 ASP cc_start: 0.7644 (t70) cc_final: 0.6766 (t0) REVERT: C 285 LEU cc_start: 0.8613 (tt) cc_final: 0.8382 (tt) REVERT: R 51 LEU cc_start: 0.8067 (mt) cc_final: 0.7740 (mp) REVERT: R 158 TRP cc_start: 0.8097 (t60) cc_final: 0.7684 (t60) REVERT: R 172 TRP cc_start: 0.6680 (m100) cc_final: 0.6470 (m100) outliers start: 7 outliers final: 4 residues processed: 159 average time/residue: 0.1186 time to fit residues: 23.3450 Evaluate side-chains 151 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 147 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.117224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.100986 restraints weight = 9332.060| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.16 r_work: 0.3120 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6579 Z= 0.163 Angle : 0.552 5.747 8966 Z= 0.287 Chirality : 0.043 0.132 1061 Planarity : 0.003 0.036 1122 Dihedral : 4.268 23.680 927 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.18 % Allowed : 10.73 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.30), residues: 844 helix: 1.78 (0.28), residues: 359 sheet: -0.16 (0.40), residues: 173 loop : -1.32 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 304 TYR 0.012 0.001 TYR C 59 PHE 0.012 0.001 PHE R 178 TRP 0.015 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6578) covalent geometry : angle 0.55179 ( 8964) SS BOND : bond 0.00437 ( 1) SS BOND : angle 0.98245 ( 2) hydrogen bonds : bond 0.04645 ( 344) hydrogen bonds : angle 4.40900 ( 978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.173 Fit side-chains REVERT: B 8 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6760 (tm-30) REVERT: B 28 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6924 (mm-30) REVERT: B 32 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7406 (mtm-85) REVERT: C 68 ARG cc_start: 0.8405 (ttt180) cc_final: 0.7741 (ttt-90) REVERT: C 76 ASP cc_start: 0.7550 (p0) cc_final: 0.7280 (p0) REVERT: C 134 ARG cc_start: 0.7224 (pmt-80) cc_final: 0.6754 (pmt-80) REVERT: C 258 ASP cc_start: 0.7674 (t70) cc_final: 0.6800 (t0) REVERT: C 277 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8137 (t) REVERT: C 285 LEU cc_start: 0.8503 (tt) cc_final: 0.8266 (tt) REVERT: C 318 LEU cc_start: 0.8091 (tt) cc_final: 0.7871 (tp) REVERT: C 336 LEU cc_start: 0.8233 (mp) cc_final: 0.8014 (mp) REVERT: R 51 LEU cc_start: 0.8120 (mt) cc_final: 0.7781 (mp) REVERT: R 158 TRP cc_start: 0.8171 (t60) cc_final: 0.7837 (t60) outliers start: 14 outliers final: 6 residues processed: 162 average time/residue: 0.1071 time to fit residues: 21.1731 Evaluate side-chains 158 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 0.0570 chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS C 239 ASN R 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099033 restraints weight = 9538.012| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.30 r_work: 0.3083 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6579 Z= 0.172 Angle : 0.544 5.351 8966 Z= 0.284 Chirality : 0.042 0.134 1061 Planarity : 0.003 0.035 1122 Dihedral : 4.262 24.088 927 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.95 % Allowed : 13.37 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.30), residues: 844 helix: 1.99 (0.28), residues: 359 sheet: -0.16 (0.40), residues: 175 loop : -1.27 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 304 TYR 0.012 0.001 TYR C 59 PHE 0.013 0.001 PHE C 278 TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6578) covalent geometry : angle 0.54358 ( 8964) SS BOND : bond 0.00570 ( 1) SS BOND : angle 1.16227 ( 2) hydrogen bonds : bond 0.04429 ( 344) hydrogen bonds : angle 4.25775 ( 978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.181 Fit side-chains REVERT: B 8 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6791 (tm-30) REVERT: B 28 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6922 (mm-30) REVERT: B 32 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7388 (mtm-85) REVERT: C 68 ARG cc_start: 0.8370 (ttt180) cc_final: 0.7680 (ttt-90) REVERT: C 76 ASP cc_start: 0.7582 (p0) cc_final: 0.7269 (p0) REVERT: C 134 ARG cc_start: 0.7207 (pmt-80) cc_final: 0.6644 (pmt-80) REVERT: C 188 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7909 (mtp) REVERT: C 258 ASP cc_start: 0.7712 (t70) cc_final: 0.6822 (t0) REVERT: C 285 LEU cc_start: 0.8510 (tt) cc_final: 0.8251 (tt) REVERT: C 318 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8011 (tp) REVERT: C 336 LEU cc_start: 0.8237 (mp) cc_final: 0.8008 (mp) REVERT: C 338 ILE cc_start: 0.8594 (mm) cc_final: 0.8238 (mm) REVERT: R 30 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6752 (mm) REVERT: R 49 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8398 (mp) REVERT: R 51 LEU cc_start: 0.8032 (mt) cc_final: 0.7696 (mp) outliers start: 19 outliers final: 10 residues processed: 156 average time/residue: 0.1006 time to fit residues: 19.2282 Evaluate side-chains 160 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 68 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099612 restraints weight = 9581.800| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.23 r_work: 0.3107 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6579 Z= 0.139 Angle : 0.520 5.291 8966 Z= 0.273 Chirality : 0.041 0.131 1061 Planarity : 0.003 0.040 1122 Dihedral : 4.147 24.417 927 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.33 % Allowed : 15.71 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.30), residues: 844 helix: 2.25 (0.29), residues: 355 sheet: -0.09 (0.42), residues: 164 loop : -1.24 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 15 TYR 0.009 0.001 TYR C 59 PHE 0.011 0.001 PHE R 178 TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6578) covalent geometry : angle 0.52032 ( 8964) SS BOND : bond 0.00460 ( 1) SS BOND : angle 0.64461 ( 2) hydrogen bonds : bond 0.04030 ( 344) hydrogen bonds : angle 4.10694 ( 978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.175 Fit side-chains REVERT: B 8 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6770 (tm-30) REVERT: B 28 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6998 (mm-30) REVERT: B 32 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7407 (mtm-85) REVERT: B 194 ARG cc_start: 0.7895 (ttp-170) cc_final: 0.7478 (tmm-80) REVERT: C 68 ARG cc_start: 0.8378 (ttt180) cc_final: 0.7649 (ttt-90) REVERT: C 76 ASP cc_start: 0.7582 (p0) cc_final: 0.7299 (p0) REVERT: C 134 ARG cc_start: 0.7228 (pmt-80) cc_final: 0.6707 (pmt-80) REVERT: C 188 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7919 (mtp) REVERT: C 258 ASP cc_start: 0.7702 (t70) cc_final: 0.6828 (t0) REVERT: C 283 ARG cc_start: 0.8233 (tpp80) cc_final: 0.8018 (tpt-90) REVERT: C 285 LEU cc_start: 0.8422 (tt) cc_final: 0.8187 (tt) REVERT: C 336 LEU cc_start: 0.8223 (mp) cc_final: 0.8007 (mp) REVERT: C 338 ILE cc_start: 0.8605 (mm) cc_final: 0.8239 (mm) REVERT: R 49 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8387 (mp) REVERT: R 51 LEU cc_start: 0.8042 (mt) cc_final: 0.7700 (mp) outliers start: 15 outliers final: 8 residues processed: 154 average time/residue: 0.1095 time to fit residues: 20.4678 Evaluate side-chains 156 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 18 optimal weight: 0.0670 chunk 2 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.0270 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.116604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099682 restraints weight = 9473.077| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.32 r_work: 0.3088 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6579 Z= 0.138 Angle : 0.509 5.447 8966 Z= 0.268 Chirality : 0.041 0.130 1061 Planarity : 0.003 0.039 1122 Dihedral : 4.076 24.270 927 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.64 % Allowed : 16.64 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.30), residues: 844 helix: 2.39 (0.28), residues: 356 sheet: -0.10 (0.42), residues: 164 loop : -1.21 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 15 TYR 0.009 0.001 TYR B 243 PHE 0.011 0.001 PHE R 178 TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6578) covalent geometry : angle 0.50943 ( 8964) SS BOND : bond 0.00465 ( 1) SS BOND : angle 0.63244 ( 2) hydrogen bonds : bond 0.03959 ( 344) hydrogen bonds : angle 4.01840 ( 978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.264 Fit side-chains REVERT: B 8 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6794 (tm-30) REVERT: B 28 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7004 (mm-30) REVERT: B 31 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7905 (ttp80) REVERT: B 32 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7342 (mtm-85) REVERT: C 59 TYR cc_start: 0.8076 (m-80) cc_final: 0.7865 (m-80) REVERT: C 68 ARG cc_start: 0.8321 (ttt180) cc_final: 0.7610 (ttt-90) REVERT: C 76 ASP cc_start: 0.7583 (p0) cc_final: 0.7277 (p0) REVERT: C 88 ASN cc_start: 0.7987 (m110) cc_final: 0.7759 (m110) REVERT: C 134 ARG cc_start: 0.7230 (pmt-80) cc_final: 0.6719 (pmt-80) REVERT: C 188 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7936 (mtp) REVERT: C 258 ASP cc_start: 0.7695 (t70) cc_final: 0.6839 (t0) REVERT: C 268 ASN cc_start: 0.7838 (m-40) cc_final: 0.7564 (m-40) REVERT: C 285 LEU cc_start: 0.8424 (tt) cc_final: 0.8176 (tt) REVERT: C 289 TYR cc_start: 0.8316 (m-80) cc_final: 0.8112 (m-80) REVERT: C 304 ARG cc_start: 0.7974 (ttt-90) cc_final: 0.7669 (ttt-90) REVERT: C 336 LEU cc_start: 0.8197 (mp) cc_final: 0.7980 (mp) REVERT: C 338 ILE cc_start: 0.8612 (mm) cc_final: 0.8247 (mm) REVERT: R 49 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8349 (mp) REVERT: R 51 LEU cc_start: 0.8016 (mt) cc_final: 0.7663 (mp) outliers start: 17 outliers final: 9 residues processed: 163 average time/residue: 0.1063 time to fit residues: 21.3128 Evaluate side-chains 164 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 0.0170 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103151 restraints weight = 9202.385| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.07 r_work: 0.3118 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6579 Z= 0.132 Angle : 0.513 8.942 8966 Z= 0.267 Chirality : 0.041 0.211 1061 Planarity : 0.003 0.041 1122 Dihedral : 4.040 24.127 927 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.49 % Allowed : 17.26 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.30), residues: 844 helix: 2.51 (0.28), residues: 356 sheet: -0.21 (0.41), residues: 164 loop : -1.17 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 15 TYR 0.008 0.001 TYR B 243 PHE 0.011 0.001 PHE R 178 TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6578) covalent geometry : angle 0.51252 ( 8964) SS BOND : bond 0.00429 ( 1) SS BOND : angle 0.51791 ( 2) hydrogen bonds : bond 0.03867 ( 344) hydrogen bonds : angle 3.96756 ( 978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.169 Fit side-chains REVERT: B 8 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6767 (tm-30) REVERT: B 28 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7066 (mm-30) REVERT: B 31 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7849 (ttp80) REVERT: B 32 ARG cc_start: 0.7768 (mtm-85) cc_final: 0.7388 (mtm-85) REVERT: B 145 LYS cc_start: 0.8343 (mtpp) cc_final: 0.8044 (mtpt) REVERT: C 59 TYR cc_start: 0.8033 (m-80) cc_final: 0.7814 (m-80) REVERT: C 68 ARG cc_start: 0.8288 (ttt180) cc_final: 0.7576 (ttt-90) REVERT: C 76 ASP cc_start: 0.7541 (p0) cc_final: 0.7276 (p0) REVERT: C 134 ARG cc_start: 0.7222 (pmt-80) cc_final: 0.6662 (pmt-80) REVERT: C 188 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7885 (mtp) REVERT: C 258 ASP cc_start: 0.7658 (t70) cc_final: 0.6797 (t0) REVERT: C 268 ASN cc_start: 0.7788 (m-40) cc_final: 0.7514 (m-40) REVERT: C 283 ARG cc_start: 0.8254 (tpp80) cc_final: 0.7828 (tpt-90) REVERT: C 285 LEU cc_start: 0.8356 (tt) cc_final: 0.8097 (tt) REVERT: C 318 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8048 (mp) REVERT: C 338 ILE cc_start: 0.8584 (mm) cc_final: 0.8213 (mm) REVERT: R 30 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6447 (mm) REVERT: R 51 LEU cc_start: 0.8033 (mt) cc_final: 0.7681 (mp) outliers start: 16 outliers final: 10 residues processed: 164 average time/residue: 0.0978 time to fit residues: 19.8385 Evaluate side-chains 164 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098018 restraints weight = 9475.562| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.25 r_work: 0.3062 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6579 Z= 0.240 Angle : 0.592 8.124 8966 Z= 0.307 Chirality : 0.044 0.142 1061 Planarity : 0.004 0.045 1122 Dihedral : 4.426 21.436 927 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.33 % Allowed : 18.35 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.30), residues: 844 helix: 2.17 (0.28), residues: 362 sheet: -0.35 (0.41), residues: 169 loop : -1.30 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 15 TYR 0.012 0.002 TYR C 105 PHE 0.017 0.002 PHE C 278 TRP 0.017 0.002 TRP C 82 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 6578) covalent geometry : angle 0.59158 ( 8964) SS BOND : bond 0.00709 ( 1) SS BOND : angle 0.89300 ( 2) hydrogen bonds : bond 0.04705 ( 344) hydrogen bonds : angle 4.24439 ( 978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.157 Fit side-chains REVERT: B 8 GLU cc_start: 0.7334 (tm-30) cc_final: 0.6864 (tm-30) REVERT: B 28 GLU cc_start: 0.7268 (mm-30) cc_final: 0.7036 (mm-30) REVERT: B 32 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.7517 (mtm-85) REVERT: B 73 LYS cc_start: 0.8059 (mttm) cc_final: 0.7722 (mttm) REVERT: C 68 ARG cc_start: 0.8373 (ttt180) cc_final: 0.7639 (ttt-90) REVERT: C 76 ASP cc_start: 0.7563 (p0) cc_final: 0.7250 (p0) REVERT: C 134 ARG cc_start: 0.7258 (pmt-80) cc_final: 0.6620 (pmt-80) REVERT: C 258 ASP cc_start: 0.7692 (t70) cc_final: 0.6812 (t0) REVERT: C 283 ARG cc_start: 0.8328 (tpp80) cc_final: 0.7960 (tpt-90) REVERT: C 285 LEU cc_start: 0.8488 (tt) cc_final: 0.8238 (tt) REVERT: C 289 TYR cc_start: 0.8441 (m-80) cc_final: 0.7971 (m-80) REVERT: C 318 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8110 (mp) REVERT: C 338 ILE cc_start: 0.8628 (mm) cc_final: 0.8247 (mt) REVERT: R 51 LEU cc_start: 0.8017 (mt) cc_final: 0.7695 (mp) outliers start: 15 outliers final: 12 residues processed: 154 average time/residue: 0.1092 time to fit residues: 20.3844 Evaluate side-chains 161 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 77 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102783 restraints weight = 9313.235| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.05 r_work: 0.3107 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6579 Z= 0.149 Angle : 0.536 7.408 8966 Z= 0.277 Chirality : 0.042 0.133 1061 Planarity : 0.003 0.041 1122 Dihedral : 4.230 23.091 927 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.18 % Allowed : 18.82 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.30), residues: 844 helix: 2.45 (0.29), residues: 355 sheet: -0.23 (0.41), residues: 166 loop : -1.18 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 15 TYR 0.010 0.001 TYR C 59 PHE 0.012 0.001 PHE R 178 TRP 0.015 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6578) covalent geometry : angle 0.53634 ( 8964) SS BOND : bond 0.00478 ( 1) SS BOND : angle 0.47122 ( 2) hydrogen bonds : bond 0.04058 ( 344) hydrogen bonds : angle 4.05937 ( 978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.204 Fit side-chains REVERT: B 8 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6798 (tm-30) REVERT: B 28 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6974 (mm-30) REVERT: B 32 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7403 (mtm-85) REVERT: B 145 LYS cc_start: 0.8362 (mtpp) cc_final: 0.8072 (mtpt) REVERT: C 68 ARG cc_start: 0.8309 (ttt180) cc_final: 0.7559 (ttt-90) REVERT: C 76 ASP cc_start: 0.7507 (p0) cc_final: 0.7202 (p0) REVERT: C 134 ARG cc_start: 0.7185 (pmt-80) cc_final: 0.6620 (pmt-80) REVERT: C 189 SER cc_start: 0.8180 (p) cc_final: 0.7862 (t) REVERT: C 258 ASP cc_start: 0.7642 (t70) cc_final: 0.6759 (t0) REVERT: C 283 ARG cc_start: 0.8286 (tpp80) cc_final: 0.7953 (tpt-90) REVERT: C 285 LEU cc_start: 0.8395 (tt) cc_final: 0.8130 (tt) REVERT: C 289 TYR cc_start: 0.8397 (m-80) cc_final: 0.7963 (m-80) REVERT: C 318 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8036 (mp) REVERT: C 338 ILE cc_start: 0.8580 (mm) cc_final: 0.8227 (mm) REVERT: R 51 LEU cc_start: 0.8007 (mt) cc_final: 0.7666 (mp) outliers start: 14 outliers final: 10 residues processed: 162 average time/residue: 0.1022 time to fit residues: 20.0668 Evaluate side-chains 164 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.0570 chunk 60 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101786 restraints weight = 9193.679| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.16 r_work: 0.3106 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6579 Z= 0.160 Angle : 0.550 7.296 8966 Z= 0.286 Chirality : 0.042 0.135 1061 Planarity : 0.004 0.043 1122 Dihedral : 4.247 23.288 927 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.71 % Allowed : 18.97 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.30), residues: 844 helix: 2.49 (0.29), residues: 355 sheet: -0.29 (0.40), residues: 170 loop : -1.16 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 15 TYR 0.011 0.001 TYR C 59 PHE 0.012 0.001 PHE R 178 TRP 0.015 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 6578) covalent geometry : angle 0.54962 ( 8964) SS BOND : bond 0.00514 ( 1) SS BOND : angle 0.60077 ( 2) hydrogen bonds : bond 0.04090 ( 344) hydrogen bonds : angle 4.06181 ( 978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.229 Fit side-chains REVERT: B 8 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6802 (tm-30) REVERT: B 28 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7079 (mm-30) REVERT: B 32 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7463 (mtm-85) REVERT: B 145 LYS cc_start: 0.8427 (mtpp) cc_final: 0.8159 (mtpt) REVERT: C 68 ARG cc_start: 0.8364 (ttt180) cc_final: 0.7644 (ttt-90) REVERT: C 76 ASP cc_start: 0.7536 (p0) cc_final: 0.7262 (p0) REVERT: C 134 ARG cc_start: 0.7235 (pmt-80) cc_final: 0.6697 (pmt-80) REVERT: C 258 ASP cc_start: 0.7693 (t70) cc_final: 0.6854 (t0) REVERT: C 283 ARG cc_start: 0.8334 (tpp80) cc_final: 0.8019 (tpt-90) REVERT: C 285 LEU cc_start: 0.8458 (tt) cc_final: 0.8210 (tt) REVERT: C 289 TYR cc_start: 0.8441 (m-80) cc_final: 0.8041 (m-80) REVERT: C 318 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8048 (mp) REVERT: R 30 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6721 (mm) REVERT: R 51 LEU cc_start: 0.8067 (mt) cc_final: 0.7712 (mp) outliers start: 11 outliers final: 9 residues processed: 156 average time/residue: 0.1086 time to fit residues: 20.7016 Evaluate side-chains 162 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 77 optimal weight: 0.0470 chunk 74 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100209 restraints weight = 9632.842| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.24 r_work: 0.3096 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6579 Z= 0.132 Angle : 0.522 7.007 8966 Z= 0.271 Chirality : 0.041 0.132 1061 Planarity : 0.003 0.040 1122 Dihedral : 4.124 23.851 927 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.87 % Allowed : 18.51 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.30), residues: 844 helix: 2.60 (0.29), residues: 356 sheet: -0.25 (0.40), residues: 170 loop : -1.14 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 15 TYR 0.009 0.001 TYR C 59 PHE 0.012 0.001 PHE R 178 TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6578) covalent geometry : angle 0.52188 ( 8964) SS BOND : bond 0.00432 ( 1) SS BOND : angle 0.38226 ( 2) hydrogen bonds : bond 0.03803 ( 344) hydrogen bonds : angle 3.96379 ( 978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1819.30 seconds wall clock time: 31 minutes 43.19 seconds (1903.19 seconds total)