Starting phenix.real_space_refine on Sat May 2 21:05:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oxb_70965/05_2026/9oxb_70965.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oxb_70965/05_2026/9oxb_70965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oxb_70965/05_2026/9oxb_70965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oxb_70965/05_2026/9oxb_70965.map" model { file = "/net/cci-nas-00/data/ceres_data/9oxb_70965/05_2026/9oxb_70965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oxb_70965/05_2026/9oxb_70965.cif" } resolution = 3.0 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= 0.024 sd= 0.103 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 61 5.16 5 C 5479 2.51 5 N 1425 2.21 5 O 1567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8532 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1711 Classifications: {'peptide': 224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 5, 'GLU:plan': 5, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2458 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 7, 'GLN:plan1': 4, 'ARG:plan': 9, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "C" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 328 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1761 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2244 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 8, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'GOQ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 2.02, per 1000 atoms: 0.24 Number of scatterers: 8532 At special positions: 0 Unit cell: (85.848, 121.764, 124.392, 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 61 16.00 O 1567 8.00 N 1425 7.00 C 5479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " 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: 0.73 Conformation dependent library (CDL) restraints added in 337.6 milliseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 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 13 sheets defined 38.8% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.611A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.510A pdb=" N ALA A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.208A pdb=" N THR A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.627A pdb=" N ILE A 285 " --> pdb=" O HIS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.535A pdb=" N SER D 31 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.795A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 212 removed outlier: 3.911A pdb=" N VAL D 212 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 37 removed outlier: 3.533A pdb=" N LEU R 12 " --> pdb=" O ILE R 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 77 through 111 removed outlier: 3.705A pdb=" N LEU R 98 " --> pdb=" O PHE R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 123 Processing helix chain 'R' and resid 124 through 135 Processing helix chain 'R' and resid 136 through 154 Processing helix chain 'R' and resid 167 through 210 Proline residue: R 187 - end of helix Processing helix chain 'R' and resid 218 through 250 Processing helix chain 'R' and resid 259 through 268 Processing helix chain 'R' and resid 270 through 281 removed outlier: 3.737A pdb=" N HIS R 275 " --> pdb=" O TYR R 271 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 283 through 298 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 4.070A pdb=" N CYS A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE A 221 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.642A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.778A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.885A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.547A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.785A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.619A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.624A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.563A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.214A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.566A pdb=" N ALA D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 135 through 136 removed outlier: 3.671A pdb=" N GLU D 234 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 177 " --> pdb=" O TRP D 164 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU D 166 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU D 175 " --> pdb=" O LEU D 166 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1341 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: 1.42 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1586 1.33 - 1.45: 2250 1.45 - 1.57: 4787 1.57 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 8714 Sorted by residual: bond pdb=" N ILE R 110 " pdb=" CA ILE R 110 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.57e+00 bond pdb=" N LYS R 109 " pdb=" CA LYS R 109 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.49e+00 bond pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.21e+00 bond pdb=" N LEU R 108 " pdb=" CA LEU R 108 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 4.79e+00 bond pdb=" N ARG R 268 " pdb=" CA ARG R 268 " ideal model delta sigma weight residual 1.459 1.484 -0.026 1.28e-02 6.10e+03 4.09e+00 ... (remaining 8709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 11537 1.43 - 2.86: 242 2.86 - 4.29: 52 4.29 - 5.72: 9 5.72 - 7.15: 4 Bond angle restraints: 11844 Sorted by residual: angle pdb=" C LYS A 192 " pdb=" CA LYS A 192 " pdb=" CB LYS A 192 " ideal model delta sigma weight residual 117.23 110.08 7.15 1.36e+00 5.41e-01 2.77e+01 angle pdb=" CA LYS A 192 " pdb=" C LYS A 192 " pdb=" N ASP A 193 " ideal model delta sigma weight residual 119.98 116.80 3.18 8.50e-01 1.38e+00 1.40e+01 angle pdb=" CA ASP A 350 " pdb=" CB ASP A 350 " pdb=" CG ASP A 350 " ideal model delta sigma weight residual 112.60 115.74 -3.14 1.00e+00 1.00e+00 9.85e+00 angle pdb=" CA LYS R 109 " pdb=" C LYS R 109 " pdb=" O LYS R 109 " ideal model delta sigma weight residual 120.82 117.74 3.08 1.05e+00 9.07e-01 8.62e+00 angle pdb=" CA ILE R 110 " pdb=" C ILE R 110 " pdb=" O ILE R 110 " ideal model delta sigma weight residual 120.78 117.43 3.35 1.25e+00 6.40e-01 7.18e+00 ... (remaining 11839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4694 17.63 - 35.26: 329 35.26 - 52.89: 54 52.89 - 70.52: 12 70.52 - 88.15: 5 Dihedral angle restraints: 5094 sinusoidal: 1822 harmonic: 3272 Sorted by residual: dihedral pdb=" CB CYS D 147 " pdb=" SG CYS D 147 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual -86.00 -174.00 88.00 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CA PRO R 259 " pdb=" C PRO R 259 " pdb=" N VAL R 260 " pdb=" CA VAL R 260 " ideal model delta harmonic sigma weight residual -180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA TYR D 178 " pdb=" C TYR D 178 " pdb=" N ARG D 179 " pdb=" CA ARG D 179 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 836 0.031 - 0.061: 365 0.061 - 0.092: 104 0.092 - 0.122: 66 0.122 - 0.153: 11 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA PRO D 224 " pdb=" N PRO D 224 " pdb=" C PRO D 224 " pdb=" CB PRO D 224 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA ILE D 177 " pdb=" N ILE D 177 " pdb=" C ILE D 177 " pdb=" CB ILE D 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1379 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 135 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO R 136 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO R 136 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 136 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 5 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO R 6 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO R 6 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 6 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 268 " -0.157 9.50e-02 1.11e+02 7.05e-02 3.05e+00 pdb=" NE ARG R 268 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG R 268 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG R 268 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 268 " -0.005 2.00e-02 2.50e+03 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 5 2.59 - 3.17: 6857 3.17 - 3.74: 13391 3.74 - 4.32: 18580 4.32 - 4.90: 31572 Nonbonded interactions: 70405 Sorted by model distance: nonbonded pdb=" OE2 GLU R 151 " pdb=" O HOH R 601 " model vdw 2.009 3.040 nonbonded pdb=" ND2 ASN R 65 " pdb=" O HOH R 602 " model vdw 2.356 3.120 nonbonded pdb=" CE1 PHE R 252 " pdb=" O HOH R 604 " model vdw 2.473 3.340 nonbonded pdb=" NH1 ARG R 268 " pdb=" O5 GOQ R 501 " model vdw 2.484 3.120 nonbonded pdb=" O SER R 244 " pdb=" NH2 ARG R 268 " model vdw 2.527 3.120 ... (remaining 70400 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.420 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:8.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 : 0.003 0.039 8715 Z= 0.160 Angle : 0.537 7.154 11846 Z= 0.296 Chirality : 0.042 0.153 1382 Planarity : 0.004 0.071 1477 Dihedral : 12.760 88.149 2973 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.35 (0.25), residues: 1112 helix: 2.06 (0.24), residues: 403 sheet: -0.03 (0.31), residues: 260 loop : -1.34 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 98 TYR 0.018 0.001 TYR D 178 PHE 0.028 0.001 PHE R 234 TRP 0.010 0.001 TRP R 97 HIS 0.016 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8714) covalent geometry : angle 0.53685 (11844) SS BOND : bond 0.00090 ( 1) SS BOND : angle 1.26356 ( 2) hydrogen bonds : bond 0.14542 ( 468) hydrogen bonds : angle 6.21142 ( 1341) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.241 Fit side-chains REVERT: A 48 THR cc_start: 0.7936 (p) cc_final: 0.7580 (m) REVERT: A 51 LYS cc_start: 0.8450 (ptpt) cc_final: 0.8035 (mtmm) REVERT: A 305 ASN cc_start: 0.7113 (t0) cc_final: 0.6622 (m110) REVERT: B 52 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.8369 (mtt-85) REVERT: B 143 THR cc_start: 0.8586 (m) cc_final: 0.8370 (p) REVERT: B 156 GLN cc_start: 0.8647 (mt0) cc_final: 0.8394 (mt0) REVERT: C 21 MET cc_start: 0.7048 (mpp) cc_final: 0.6738 (mpp) REVERT: R 75 PHE cc_start: 0.8204 (t80) cc_final: 0.8000 (t80) REVERT: R 196 MET cc_start: 0.6812 (mmm) cc_final: 0.6433 (ttt) REVERT: R 290 PHE cc_start: 0.7385 (t80) cc_final: 0.7101 (t80) outliers start: 0 outliers final: 2 residues processed: 171 average time/residue: 0.5055 time to fit residues: 92.4712 Evaluate side-chains 124 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain R residue 145 PHE 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: 3.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.0050 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 259 GLN B 295 ASN D 182 ASN ** R 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 283 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.117972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.095674 restraints weight = 14524.053| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.09 r_work: 0.3256 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8715 Z= 0.118 Angle : 0.503 7.976 11846 Z= 0.262 Chirality : 0.040 0.134 1382 Planarity : 0.004 0.044 1477 Dihedral : 4.674 63.545 1201 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.58 % Allowed : 9.93 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.26), residues: 1112 helix: 2.79 (0.24), residues: 397 sheet: 0.33 (0.32), residues: 265 loop : -1.14 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 268 TYR 0.013 0.001 TYR D 178 PHE 0.018 0.001 PHE R 234 TRP 0.013 0.001 TRP R 97 HIS 0.009 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8714) covalent geometry : angle 0.50330 (11844) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.53930 ( 2) hydrogen bonds : bond 0.03496 ( 468) hydrogen bonds : angle 4.53685 ( 1341) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.255 Fit side-chains REVERT: A 48 THR cc_start: 0.7876 (p) cc_final: 0.7563 (m) REVERT: A 51 LYS cc_start: 0.8471 (ptpt) cc_final: 0.8083 (mtmm) REVERT: A 305 ASN cc_start: 0.7043 (t0) cc_final: 0.6580 (m110) REVERT: B 124 TYR cc_start: 0.8916 (m-80) cc_final: 0.8576 (m-80) REVERT: B 143 THR cc_start: 0.8663 (m) cc_final: 0.8389 (p) REVERT: B 156 GLN cc_start: 0.8608 (mt0) cc_final: 0.8278 (mt0) REVERT: C 21 MET cc_start: 0.6987 (mpp) cc_final: 0.6754 (mpp) REVERT: D 93 MET cc_start: 0.8721 (ttp) cc_final: 0.8395 (ttt) REVERT: R 75 PHE cc_start: 0.8235 (t80) cc_final: 0.7820 (t80) REVERT: R 134 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7636 (mm) REVERT: R 196 MET cc_start: 0.7078 (mmm) cc_final: 0.6690 (ttt) REVERT: R 290 PHE cc_start: 0.7394 (t80) cc_final: 0.7116 (t80) outliers start: 14 outliers final: 4 residues processed: 141 average time/residue: 0.5130 time to fit residues: 77.0633 Evaluate side-chains 124 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 243 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** R 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.115391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.092912 restraints weight = 14481.215| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.07 r_work: 0.3198 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8715 Z= 0.173 Angle : 0.546 9.369 11846 Z= 0.286 Chirality : 0.041 0.168 1382 Planarity : 0.004 0.044 1477 Dihedral : 4.765 71.040 1197 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.03 % Allowed : 12.30 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.88 (0.26), residues: 1112 helix: 2.59 (0.25), residues: 403 sheet: 0.34 (0.32), residues: 261 loop : -1.20 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 219 TYR 0.019 0.002 TYR D 178 PHE 0.016 0.002 PHE R 234 TRP 0.023 0.002 TRP R 281 HIS 0.007 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8714) covalent geometry : angle 0.54619 (11844) SS BOND : bond 0.00118 ( 1) SS BOND : angle 0.86453 ( 2) hydrogen bonds : bond 0.03872 ( 468) hydrogen bonds : angle 4.38154 ( 1341) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.321 Fit side-chains REVERT: A 48 THR cc_start: 0.8003 (p) cc_final: 0.7726 (m) REVERT: A 51 LYS cc_start: 0.8477 (ptpt) cc_final: 0.8101 (mtmm) REVERT: A 200 ASP cc_start: 0.8279 (t0) cc_final: 0.8038 (t0) REVERT: A 305 ASN cc_start: 0.7138 (t0) cc_final: 0.6909 (m-40) REVERT: B 75 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7477 (pt0) REVERT: B 124 TYR cc_start: 0.9006 (m-80) cc_final: 0.8719 (m-80) REVERT: B 143 THR cc_start: 0.8708 (m) cc_final: 0.8377 (p) REVERT: B 156 GLN cc_start: 0.8702 (mt0) cc_final: 0.8445 (mt0) REVERT: C 21 MET cc_start: 0.7120 (mpp) cc_final: 0.6862 (mpp) REVERT: D 90 ASP cc_start: 0.8547 (m-30) cc_final: 0.8095 (m-30) REVERT: D 93 MET cc_start: 0.8885 (ttp) cc_final: 0.8604 (ttt) REVERT: R 67 TYR cc_start: 0.8076 (t80) cc_final: 0.7703 (t80) REVERT: R 75 PHE cc_start: 0.8232 (t80) cc_final: 0.7790 (t80) REVERT: R 134 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7533 (mm) REVERT: R 196 MET cc_start: 0.7660 (mmm) cc_final: 0.7314 (ttt) REVERT: R 290 PHE cc_start: 0.7422 (t80) cc_final: 0.7108 (t80) outliers start: 18 outliers final: 7 residues processed: 140 average time/residue: 0.4951 time to fit residues: 74.5122 Evaluate side-chains 128 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 243 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** R 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.115892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.093874 restraints weight = 14899.874| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.09 r_work: 0.3207 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8715 Z= 0.130 Angle : 0.507 8.995 11846 Z= 0.265 Chirality : 0.040 0.145 1382 Planarity : 0.003 0.044 1477 Dihedral : 4.661 71.156 1197 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.69 % Allowed : 15.69 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1112 helix: 2.78 (0.25), residues: 405 sheet: 0.43 (0.32), residues: 261 loop : -1.18 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.016 0.001 TYR D 178 PHE 0.021 0.002 PHE R 36 TRP 0.011 0.001 TRP R 97 HIS 0.006 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8714) covalent geometry : angle 0.50745 (11844) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.43465 ( 2) hydrogen bonds : bond 0.03375 ( 468) hydrogen bonds : angle 4.20919 ( 1341) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.363 Fit side-chains REVERT: A 51 LYS cc_start: 0.8480 (ptpt) cc_final: 0.8119 (mtmm) REVERT: A 200 ASP cc_start: 0.8296 (t0) cc_final: 0.8008 (t0) REVERT: A 305 ASN cc_start: 0.7156 (t0) cc_final: 0.6907 (m-40) REVERT: A 350 ASP cc_start: 0.7784 (m-30) cc_final: 0.7534 (m-30) REVERT: B 124 TYR cc_start: 0.8998 (m-80) cc_final: 0.8625 (m-80) REVERT: C 21 MET cc_start: 0.7152 (mpp) cc_final: 0.6903 (mpp) REVERT: D 90 ASP cc_start: 0.8521 (m-30) cc_final: 0.8090 (m-30) REVERT: D 93 MET cc_start: 0.8857 (ttp) cc_final: 0.8625 (ttt) REVERT: R 67 TYR cc_start: 0.8091 (t80) cc_final: 0.7693 (t80) REVERT: R 75 PHE cc_start: 0.8226 (t80) cc_final: 0.7793 (t80) REVERT: R 134 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7480 (mm) REVERT: R 196 MET cc_start: 0.7700 (mmm) cc_final: 0.7339 (ttt) REVERT: R 290 PHE cc_start: 0.7428 (t80) cc_final: 0.7123 (t80) outliers start: 15 outliers final: 6 residues processed: 136 average time/residue: 0.5034 time to fit residues: 73.5083 Evaluate side-chains 126 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 243 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.112812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.090805 restraints weight = 14812.758| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.07 r_work: 0.3157 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8715 Z= 0.236 Angle : 0.598 8.895 11846 Z= 0.310 Chirality : 0.043 0.180 1382 Planarity : 0.004 0.046 1477 Dihedral : 4.969 69.040 1197 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.14 % Allowed : 16.48 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.81 (0.25), residues: 1112 helix: 2.50 (0.25), residues: 405 sheet: 0.32 (0.32), residues: 263 loop : -1.25 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 219 TYR 0.021 0.002 TYR D 178 PHE 0.020 0.002 PHE R 36 TRP 0.010 0.002 TRP B 169 HIS 0.005 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 8714) covalent geometry : angle 0.59837 (11844) SS BOND : bond 0.00294 ( 1) SS BOND : angle 1.04906 ( 2) hydrogen bonds : bond 0.04004 ( 468) hydrogen bonds : angle 4.35175 ( 1341) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8502 (ptpt) cc_final: 0.8197 (mtmm) REVERT: A 200 ASP cc_start: 0.8281 (t0) cc_final: 0.7982 (t0) REVERT: A 305 ASN cc_start: 0.7134 (t0) cc_final: 0.6930 (m110) REVERT: A 350 ASP cc_start: 0.7905 (m-30) cc_final: 0.7633 (m-30) REVERT: B 259 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7450 (pm20) REVERT: B 315 VAL cc_start: 0.7963 (OUTLIER) cc_final: 0.7434 (t) REVERT: D 90 ASP cc_start: 0.8546 (m-30) cc_final: 0.8119 (m-30) REVERT: D 93 MET cc_start: 0.8904 (ttp) cc_final: 0.8676 (ttt) REVERT: R 67 TYR cc_start: 0.8143 (t80) cc_final: 0.7656 (t80) REVERT: R 75 PHE cc_start: 0.8211 (t80) cc_final: 0.7835 (t80) REVERT: R 134 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7467 (mm) REVERT: R 196 MET cc_start: 0.7825 (mmm) cc_final: 0.7546 (ttt) REVERT: R 290 PHE cc_start: 0.7518 (t80) cc_final: 0.7211 (t80) outliers start: 19 outliers final: 6 residues processed: 139 average time/residue: 0.4782 time to fit residues: 71.5962 Evaluate side-chains 132 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 243 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 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 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.114964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.093116 restraints weight = 14736.466| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.06 r_work: 0.3196 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8715 Z= 0.125 Angle : 0.507 8.825 11846 Z= 0.265 Chirality : 0.040 0.145 1382 Planarity : 0.003 0.044 1477 Dihedral : 4.719 69.453 1197 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.92 % Allowed : 16.37 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1112 helix: 2.77 (0.25), residues: 405 sheet: 0.46 (0.32), residues: 260 loop : -1.19 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.019 0.001 TYR D 178 PHE 0.022 0.001 PHE R 36 TRP 0.011 0.001 TRP R 88 HIS 0.006 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8714) covalent geometry : angle 0.50737 (11844) SS BOND : bond 0.00025 ( 1) SS BOND : angle 0.25786 ( 2) hydrogen bonds : bond 0.03368 ( 468) hydrogen bonds : angle 4.16654 ( 1341) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.322 Fit side-chains REVERT: A 51 LYS cc_start: 0.8516 (ptpt) cc_final: 0.8211 (mtmm) REVERT: A 200 ASP cc_start: 0.8301 (t0) cc_final: 0.8066 (t0) REVERT: A 248 LYS cc_start: 0.7729 (mtmm) cc_final: 0.7349 (mtpt) REVERT: A 305 ASN cc_start: 0.7155 (t0) cc_final: 0.6947 (m110) REVERT: A 350 ASP cc_start: 0.7820 (m-30) cc_final: 0.7562 (m-30) REVERT: B 315 VAL cc_start: 0.7985 (OUTLIER) cc_final: 0.7443 (t) REVERT: C 21 MET cc_start: 0.7255 (mpp) cc_final: 0.6937 (mpp) REVERT: D 90 ASP cc_start: 0.8536 (m-30) cc_final: 0.8107 (m-30) REVERT: R 38 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7252 (tpm170) REVERT: R 67 TYR cc_start: 0.8140 (t80) cc_final: 0.7659 (t80) REVERT: R 75 PHE cc_start: 0.8149 (t80) cc_final: 0.7757 (t80) REVERT: R 126 LYS cc_start: 0.6552 (mmtp) cc_final: 0.6210 (tptp) REVERT: R 134 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7389 (mm) REVERT: R 196 MET cc_start: 0.7764 (mmm) cc_final: 0.7512 (ttt) REVERT: R 234 PHE cc_start: 0.7789 (t80) cc_final: 0.7114 (t80) REVERT: R 290 PHE cc_start: 0.7535 (t80) cc_final: 0.7231 (t80) outliers start: 17 outliers final: 5 residues processed: 137 average time/residue: 0.4935 time to fit residues: 72.5378 Evaluate side-chains 129 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 243 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.113414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.091527 restraints weight = 14813.083| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.06 r_work: 0.3170 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8715 Z= 0.192 Angle : 0.556 10.034 11846 Z= 0.288 Chirality : 0.042 0.165 1382 Planarity : 0.004 0.044 1477 Dihedral : 4.834 67.659 1197 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.58 % Allowed : 16.93 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.93 (0.25), residues: 1112 helix: 2.62 (0.25), residues: 405 sheet: 0.35 (0.31), residues: 263 loop : -1.18 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 219 TYR 0.019 0.002 TYR D 178 PHE 0.021 0.002 PHE R 36 TRP 0.009 0.001 TRP R 88 HIS 0.005 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8714) covalent geometry : angle 0.55616 (11844) SS BOND : bond 0.00252 ( 1) SS BOND : angle 0.71817 ( 2) hydrogen bonds : bond 0.03719 ( 468) hydrogen bonds : angle 4.22134 ( 1341) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8544 (ptpt) cc_final: 0.8260 (mtmm) REVERT: A 200 ASP cc_start: 0.8278 (t0) cc_final: 0.7974 (t0) REVERT: A 248 LYS cc_start: 0.7763 (mtmm) cc_final: 0.7398 (mtpt) REVERT: A 289 GLU cc_start: 0.7337 (tt0) cc_final: 0.7035 (mp0) REVERT: A 305 ASN cc_start: 0.7079 (t0) cc_final: 0.6796 (m-40) REVERT: A 350 ASP cc_start: 0.7882 (m-30) cc_final: 0.7616 (m-30) REVERT: B 75 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7494 (pt0) REVERT: B 259 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7430 (pm20) REVERT: B 315 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7507 (t) REVERT: D 90 ASP cc_start: 0.8539 (m-30) cc_final: 0.8112 (m-30) REVERT: R 38 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7251 (tpm170) REVERT: R 67 TYR cc_start: 0.8133 (t80) cc_final: 0.7630 (t80) REVERT: R 75 PHE cc_start: 0.8165 (t80) cc_final: 0.7810 (t80) REVERT: R 126 LYS cc_start: 0.6542 (mmtp) cc_final: 0.6162 (tptp) REVERT: R 134 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7417 (mm) REVERT: R 196 MET cc_start: 0.7850 (mmm) cc_final: 0.7542 (ttt) REVERT: R 290 PHE cc_start: 0.7521 (t80) cc_final: 0.7210 (t80) outliers start: 14 outliers final: 7 residues processed: 133 average time/residue: 0.5204 time to fit residues: 74.2249 Evaluate side-chains 133 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 243 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 41 optimal weight: 0.0670 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 0.0570 chunk 105 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 107 optimal weight: 0.0970 chunk 91 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.115760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.093720 restraints weight = 14635.376| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.06 r_work: 0.3220 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8715 Z= 0.102 Angle : 0.488 8.695 11846 Z= 0.256 Chirality : 0.040 0.130 1382 Planarity : 0.003 0.044 1477 Dihedral : 4.566 67.418 1197 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.58 % Allowed : 17.72 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.26), residues: 1112 helix: 2.92 (0.25), residues: 405 sheet: 0.57 (0.31), residues: 263 loop : -1.07 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.017 0.001 TYR D 178 PHE 0.023 0.001 PHE R 36 TRP 0.012 0.001 TRP R 88 HIS 0.006 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8714) covalent geometry : angle 0.48852 (11844) SS BOND : bond 0.00097 ( 1) SS BOND : angle 0.20032 ( 2) hydrogen bonds : bond 0.03174 ( 468) hydrogen bonds : angle 4.06758 ( 1341) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.348 Fit side-chains REVERT: A 51 LYS cc_start: 0.8550 (ptpt) cc_final: 0.8261 (mtmm) REVERT: A 200 ASP cc_start: 0.8237 (t0) cc_final: 0.7987 (t0) REVERT: A 248 LYS cc_start: 0.7744 (mtmm) cc_final: 0.7386 (mtpt) REVERT: A 289 GLU cc_start: 0.7328 (tt0) cc_final: 0.7026 (mp0) REVERT: A 305 ASN cc_start: 0.7074 (t0) cc_final: 0.6778 (m110) REVERT: B 315 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7399 (t) REVERT: C 21 MET cc_start: 0.7260 (mpp) cc_final: 0.6958 (mpp) REVERT: D 90 ASP cc_start: 0.8513 (m-30) cc_final: 0.8137 (m-30) REVERT: D 148 ARG cc_start: 0.8158 (mmp80) cc_final: 0.7939 (mmm160) REVERT: R 38 ARG cc_start: 0.7700 (ttm-80) cc_final: 0.7234 (tpm170) REVERT: R 67 TYR cc_start: 0.8088 (t80) cc_final: 0.7593 (t80) REVERT: R 75 PHE cc_start: 0.8105 (t80) cc_final: 0.7744 (t80) REVERT: R 126 LYS cc_start: 0.6590 (mmtp) cc_final: 0.6191 (tptp) REVERT: R 132 MET cc_start: 0.7100 (mpp) cc_final: 0.6757 (mmt) REVERT: R 196 MET cc_start: 0.7805 (mmm) cc_final: 0.7536 (ttt) REVERT: R 290 PHE cc_start: 0.7651 (t80) cc_final: 0.7361 (t80) outliers start: 14 outliers final: 5 residues processed: 137 average time/residue: 0.5426 time to fit residues: 79.5154 Evaluate side-chains 124 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 243 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN R 24 ASN R 283 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.115536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.093773 restraints weight = 14745.327| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.06 r_work: 0.3204 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8715 Z= 0.123 Angle : 0.508 10.191 11846 Z= 0.264 Chirality : 0.040 0.143 1382 Planarity : 0.003 0.043 1477 Dihedral : 4.546 65.152 1197 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.13 % Allowed : 18.17 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.26), residues: 1112 helix: 2.91 (0.25), residues: 405 sheet: 0.58 (0.31), residues: 265 loop : -1.09 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.017 0.001 TYR D 178 PHE 0.022 0.001 PHE R 36 TRP 0.010 0.001 TRP R 88 HIS 0.004 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8714) covalent geometry : angle 0.50789 (11844) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.42228 ( 2) hydrogen bonds : bond 0.03259 ( 468) hydrogen bonds : angle 4.04544 ( 1341) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.338 Fit side-chains REVERT: A 51 LYS cc_start: 0.8561 (ptpt) cc_final: 0.8290 (mtmm) REVERT: A 197 ARG cc_start: 0.8357 (mtm110) cc_final: 0.8033 (mtp180) REVERT: A 248 LYS cc_start: 0.7721 (mtmm) cc_final: 0.7411 (mtpt) REVERT: A 289 GLU cc_start: 0.7333 (tt0) cc_final: 0.7062 (mp0) REVERT: A 305 ASN cc_start: 0.7077 (t0) cc_final: 0.6802 (m110) REVERT: B 315 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7459 (t) REVERT: C 21 MET cc_start: 0.7279 (mpp) cc_final: 0.6946 (mpp) REVERT: D 90 ASP cc_start: 0.8517 (m-30) cc_final: 0.8031 (m-30) REVERT: R 38 ARG cc_start: 0.7679 (ttm-80) cc_final: 0.7243 (tpm170) REVERT: R 67 TYR cc_start: 0.8086 (t80) cc_final: 0.7625 (t80) REVERT: R 75 PHE cc_start: 0.8094 (t80) cc_final: 0.7756 (t80) REVERT: R 126 LYS cc_start: 0.6534 (mmtp) cc_final: 0.6163 (tptp) REVERT: R 196 MET cc_start: 0.7839 (mmm) cc_final: 0.7576 (ttt) REVERT: R 290 PHE cc_start: 0.7660 (t80) cc_final: 0.7377 (t80) outliers start: 10 outliers final: 4 residues processed: 126 average time/residue: 0.5376 time to fit residues: 72.4333 Evaluate side-chains 124 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 0.0050 chunk 79 optimal weight: 0.0010 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN R 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.116299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.094594 restraints weight = 14702.858| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.06 r_work: 0.3221 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8715 Z= 0.109 Angle : 0.500 9.326 11846 Z= 0.259 Chirality : 0.040 0.147 1382 Planarity : 0.003 0.043 1477 Dihedral : 4.381 51.633 1197 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.79 % Allowed : 18.62 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.26), residues: 1112 helix: 2.95 (0.25), residues: 405 sheet: 0.63 (0.31), residues: 265 loop : -1.08 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.016 0.001 TYR D 178 PHE 0.022 0.001 PHE R 36 TRP 0.012 0.001 TRP R 88 HIS 0.005 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8714) covalent geometry : angle 0.49964 (11844) SS BOND : bond 0.00017 ( 1) SS BOND : angle 0.33236 ( 2) hydrogen bonds : bond 0.03146 ( 468) hydrogen bonds : angle 3.99645 ( 1341) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.276 Fit side-chains REVERT: A 51 LYS cc_start: 0.8513 (ptpt) cc_final: 0.8252 (mtmm) REVERT: A 197 ARG cc_start: 0.8310 (mtm110) cc_final: 0.7941 (mtp180) REVERT: A 200 ASP cc_start: 0.8199 (t0) cc_final: 0.7879 (t0) REVERT: A 248 LYS cc_start: 0.7726 (mtmm) cc_final: 0.7413 (mtpt) REVERT: A 289 GLU cc_start: 0.7351 (tt0) cc_final: 0.7046 (mp0) REVERT: A 305 ASN cc_start: 0.7058 (t0) cc_final: 0.6735 (m110) REVERT: B 315 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7425 (t) REVERT: C 21 MET cc_start: 0.7256 (mpp) cc_final: 0.6929 (mpp) REVERT: D 90 ASP cc_start: 0.8505 (m-30) cc_final: 0.8070 (m-30) REVERT: R 38 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7241 (tpm170) REVERT: R 67 TYR cc_start: 0.8090 (t80) cc_final: 0.7649 (t80) REVERT: R 75 PHE cc_start: 0.8096 (t80) cc_final: 0.7748 (t80) REVERT: R 132 MET cc_start: 0.6940 (mpp) cc_final: 0.6723 (mmt) REVERT: R 196 MET cc_start: 0.7834 (mmm) cc_final: 0.7556 (ttt) REVERT: R 234 PHE cc_start: 0.7754 (t80) cc_final: 0.7258 (t80) REVERT: R 290 PHE cc_start: 0.7656 (t80) cc_final: 0.7391 (t80) outliers start: 7 outliers final: 4 residues processed: 124 average time/residue: 0.5334 time to fit residues: 70.8285 Evaluate side-chains 121 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 75 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.115328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.093691 restraints weight = 14593.448| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.01 r_work: 0.3208 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8715 Z= 0.142 Angle : 0.531 9.443 11846 Z= 0.274 Chirality : 0.041 0.153 1382 Planarity : 0.004 0.043 1477 Dihedral : 4.462 50.692 1197 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.79 % Allowed : 18.74 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.26), residues: 1112 helix: 2.86 (0.25), residues: 405 sheet: 0.59 (0.31), residues: 265 loop : -1.08 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 219 TYR 0.018 0.001 TYR D 178 PHE 0.022 0.002 PHE R 36 TRP 0.009 0.001 TRP R 88 HIS 0.004 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8714) covalent geometry : angle 0.53080 (11844) SS BOND : bond 0.00123 ( 1) SS BOND : angle 0.47709 ( 2) hydrogen bonds : bond 0.03358 ( 468) hydrogen bonds : angle 4.03224 ( 1341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3202.81 seconds wall clock time: 55 minutes 27.72 seconds (3327.72 seconds total)