Starting phenix.real_space_refine on Mon Apr 6 09:11:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qhj_53171/04_2026/9qhj_53171_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qhj_53171/04_2026/9qhj_53171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qhj_53171/04_2026/9qhj_53171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qhj_53171/04_2026/9qhj_53171.map" model { file = "/net/cci-nas-00/data/ceres_data/9qhj_53171/04_2026/9qhj_53171_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qhj_53171/04_2026/9qhj_53171_trim.cif" } resolution = 3.4 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= 0.000 sd= 0.047 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 32 5.16 5 C 5444 2.51 5 N 1448 2.21 5 O 1472 1.98 5 H 8530 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16934 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4403 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 250} Chain: "B" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4403 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 250} Chain: "C" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4032 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 255} Chain: "D" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4032 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 255} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.28, per 1000 atoms: 0.19 Number of scatterers: 16934 At special positions: 0 Unit cell: (84.96, 82.08, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 32 16.00 P 6 15.00 Mg 2 11.99 O 1472 8.00 N 1448 7.00 C 5444 6.00 H 8530 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.44 Conformation dependent library (CDL) restraints added in 640.6 milliseconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 67.7% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 33 through 46 removed outlier: 3.665A pdb=" N TRP A 37 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 61 removed outlier: 4.043A pdb=" N GLN A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS A 59 " --> pdb=" O TRP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 90 removed outlier: 4.223A pdb=" N THR A 73 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER A 88 " --> pdb=" O GLY A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 120 Proline residue: A 100 - end of helix removed outlier: 3.672A pdb=" N ALA A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 136 through 166 removed outlier: 4.358A pdb=" N HIS A 140 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE A 158 " --> pdb=" O HIS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 176 through 202 removed outlier: 3.819A pdb=" N PHE A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 220 removed outlier: 4.709A pdb=" N PHE A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.506A pdb=" N LEU A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 230' Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 243 through 258 removed outlier: 4.303A pdb=" N HIS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 262 through 288 removed outlier: 3.793A pdb=" N TRP A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'B' and resid 34 through 46 removed outlier: 3.994A pdb=" N ARG B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 61 removed outlier: 4.044A pdb=" N GLN B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS B 59 " --> pdb=" O TRP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 90 removed outlier: 4.224A pdb=" N THR B 73 " --> pdb=" O PRO B 69 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER B 88 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 120 Proline residue: B 100 - end of helix removed outlier: 3.672A pdb=" N ALA B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 136 through 166 removed outlier: 4.357A pdb=" N HIS B 140 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE B 158 " --> pdb=" O HIS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 176 through 202 removed outlier: 3.820A pdb=" N PHE B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 220 removed outlier: 4.710A pdb=" N PHE B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 removed outlier: 3.505A pdb=" N LEU B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 230' Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 243 through 258 removed outlier: 4.302A pdb=" N HIS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 262 through 288 removed outlier: 3.792A pdb=" N TRP B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 268 " --> pdb=" O HIS B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'C' and resid 72 through 79 Processing helix chain 'C' and resid 110 through 122 Processing helix chain 'C' and resid 125 through 141 removed outlier: 4.953A pdb=" N ASP C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 136 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 154 through 168 Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.552A pdb=" N ALA C 182 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 236 through 244 Processing helix chain 'C' and resid 245 through 263 Processing helix chain 'D' and resid 72 through 79 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 125 through 141 removed outlier: 4.953A pdb=" N ASP D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE D 136 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 154 through 168 Processing helix chain 'D' and resid 179 through 183 removed outlier: 3.552A pdb=" N ALA D 182 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 211 through 219 Processing helix chain 'D' and resid 236 through 244 Processing helix chain 'D' and resid 245 through 263 Processing sheet with id=AA1, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'C' and resid 9 through 15 removed outlier: 6.537A pdb=" N ALA C 9 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG C 49 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL C 11 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C 43 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA C 34 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 95 through 98 removed outlier: 4.203A pdb=" N LEU C 175 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU C 174 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA C 208 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU C 176 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG C 60 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N MET C 223 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY C 62 " --> pdb=" O MET C 223 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE C 225 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C 64 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET C 232 " --> pdb=" O TRP C 224 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP C 226 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'D' and resid 9 through 15 removed outlier: 6.538A pdb=" N ALA D 9 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG D 49 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL D 11 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL D 43 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA D 34 " --> pdb=" O GLU D 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 95 through 98 removed outlier: 4.204A pdb=" N LEU D 175 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU D 174 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA D 208 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU D 176 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG D 60 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N MET D 223 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY D 62 " --> pdb=" O MET D 223 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE D 225 " --> pdb=" O GLY D 62 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL D 64 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET D 232 " --> pdb=" O TRP D 224 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP D 226 " --> pdb=" O ILE D 230 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1410 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: 3.89 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8526 1.03 - 1.23: 32 1.23 - 1.43: 3572 1.43 - 1.62: 4940 1.62 - 1.82: 60 Bond restraints: 17130 Sorted by residual: bond pdb=" CG MET D 157 " pdb=" HG2 MET D 157 " ideal model delta sigma weight residual 0.970 0.925 0.045 2.00e-02 2.50e+03 5.13e+00 bond pdb=" CG MET C 157 " pdb=" HG2 MET C 157 " ideal model delta sigma weight residual 0.970 0.925 0.045 2.00e-02 2.50e+03 5.13e+00 bond pdb=" CG MET C 223 " pdb=" HG2 MET C 223 " ideal model delta sigma weight residual 0.970 0.938 0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" CG MET D 223 " pdb=" HG2 MET D 223 " ideal model delta sigma weight residual 0.970 0.938 0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" CA ILE C 136 " pdb=" CB ILE C 136 " ideal model delta sigma weight residual 1.538 1.554 -0.015 1.06e-02 8.90e+03 2.01e+00 ... (remaining 17125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 30874 3.72 - 7.43: 114 7.43 - 11.15: 4 11.15 - 14.86: 4 14.86 - 18.58: 6 Bond angle restraints: 31002 Sorted by residual: angle pdb=" HE2 LYS D 30 " pdb=" CE LYS D 30 " pdb=" HE3 LYS D 30 " ideal model delta sigma weight residual 110.00 91.42 18.58 3.00e+00 1.11e-01 3.83e+01 angle pdb=" HE2 LYS C 30 " pdb=" CE LYS C 30 " pdb=" HE3 LYS C 30 " ideal model delta sigma weight residual 110.00 91.42 18.58 3.00e+00 1.11e-01 3.83e+01 angle pdb=" CD LYS C 30 " pdb=" CE LYS C 30 " pdb=" HE3 LYS C 30 " ideal model delta sigma weight residual 109.00 125.85 -16.85 3.00e+00 1.11e-01 3.16e+01 angle pdb=" CD LYS D 30 " pdb=" CE LYS D 30 " pdb=" HE3 LYS D 30 " ideal model delta sigma weight residual 109.00 125.83 -16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" NZ LYS D 30 " pdb=" CE LYS D 30 " pdb=" HE2 LYS D 30 " ideal model delta sigma weight residual 108.00 91.17 16.83 3.00e+00 1.11e-01 3.15e+01 ... (remaining 30997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7040 17.96 - 35.92: 632 35.92 - 53.88: 228 53.88 - 71.84: 60 71.84 - 89.80: 20 Dihedral angle restraints: 7980 sinusoidal: 4364 harmonic: 3616 Sorted by residual: dihedral pdb=" CA GLU A 127 " pdb=" C GLU A 127 " pdb=" N GLY A 128 " pdb=" CA GLY A 128 " ideal model delta harmonic sigma weight residual -180.00 -151.46 -28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA GLU B 127 " pdb=" C GLU B 127 " pdb=" N GLY B 128 " pdb=" CA GLY B 128 " ideal model delta harmonic sigma weight residual 180.00 -151.48 -28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA GLU C 141 " pdb=" C GLU C 141 " pdb=" N LEU C 142 " pdb=" CA LEU C 142 " ideal model delta harmonic sigma weight residual -180.00 -152.32 -27.68 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 7977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1051 0.053 - 0.106: 249 0.106 - 0.159: 30 0.159 - 0.213: 2 0.213 - 0.266: 6 Chirality restraints: 1338 Sorted by residual: chirality pdb=" C2' ATP D 502 " pdb=" C1' ATP D 502 " pdb=" C3' ATP D 502 " pdb=" O2' ATP D 502 " both_signs ideal model delta sigma weight residual False -2.68 -2.95 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C2' ATP C 502 " pdb=" C1' ATP C 502 " pdb=" C3' ATP C 502 " pdb=" O2' ATP C 502 " both_signs ideal model delta sigma weight residual False -2.68 -2.95 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C3' ATP D 502 " pdb=" C2' ATP D 502 " pdb=" C4' ATP D 502 " pdb=" O3' ATP D 502 " both_signs ideal model delta sigma weight residual False -2.63 -2.89 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1335 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 76 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C THR A 76 " 0.048 2.00e-02 2.50e+03 pdb=" O THR A 76 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY A 77 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 76 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C THR B 76 " -0.047 2.00e-02 2.50e+03 pdb=" O THR B 76 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY B 77 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 78 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.41e+00 pdb=" C SER A 78 " -0.047 2.00e-02 2.50e+03 pdb=" O SER A 78 " 0.018 2.00e-02 2.50e+03 pdb=" N THR A 79 " 0.016 2.00e-02 2.50e+03 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 4415 2.32 - 2.89: 38958 2.89 - 3.46: 44819 3.46 - 4.03: 60672 4.03 - 4.60: 92797 Nonbonded interactions: 241661 Sorted by model distance: nonbonded pdb=" H THR D 167 " pdb=" HG1 THR D 167 " model vdw 1.755 2.100 nonbonded pdb=" H THR C 167 " pdb=" HG1 THR C 167 " model vdw 1.756 2.100 nonbonded pdb="HD21 LEU C 142 " pdb=" HG2 MET C 157 " model vdw 1.805 2.440 nonbonded pdb="HD21 LEU D 142 " pdb=" HG2 MET D 157 " model vdw 1.805 2.440 nonbonded pdb=" HE2 LYS C 30 " pdb=" HZ3 LYS C 30 " model vdw 1.898 1.816 ... (remaining 241656 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 0.100 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.090 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.005 0.047 8600 Z= 0.210 Angle : 0.818 7.300 11698 Z= 0.449 Chirality : 0.047 0.266 1338 Planarity : 0.007 0.046 1454 Dihedral : 17.038 89.612 3138 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 16.44 % Favored : 83.56 % 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 are not related in a simple way. whole: -1.19 (0.25), residues: 1042 helix: -0.67 (0.20), residues: 628 sheet: -1.76 (0.51), residues: 100 loop : -0.24 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 126 TYR 0.019 0.002 TYR B 101 PHE 0.021 0.002 PHE A 91 TRP 0.022 0.002 TRP A 50 HIS 0.007 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 8600) covalent geometry : angle 0.81753 (11698) hydrogen bonds : bond 0.17123 ( 488) hydrogen bonds : angle 7.46302 ( 1410) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.7278 (m-80) cc_final: 0.7066 (m-80) REVERT: A 97 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7510 (tp30) REVERT: B 62 TYR cc_start: 0.7382 (m-80) cc_final: 0.7180 (m-80) REVERT: B 97 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7653 (tp30) REVERT: C 128 GLN cc_start: 0.7225 (mt0) cc_final: 0.7000 (mt0) REVERT: C 197 GLN cc_start: 0.7723 (mt0) cc_final: 0.7351 (mm-40) REVERT: D 100 ASP cc_start: 0.7141 (t0) cc_final: 0.6934 (t0) REVERT: D 128 GLN cc_start: 0.7338 (mt0) cc_final: 0.7116 (mt0) REVERT: D 197 GLN cc_start: 0.7598 (mt0) cc_final: 0.7322 (mm-40) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1706 time to fit residues: 28.9144 Evaluate side-chains 101 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.145037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117166 restraints weight = 28275.965| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.08 r_work: 0.3152 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8600 Z= 0.153 Angle : 0.541 4.664 11698 Z= 0.295 Chirality : 0.040 0.143 1338 Planarity : 0.004 0.037 1454 Dihedral : 9.353 84.268 1210 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.35 % Allowed : 16.78 % Favored : 81.87 % 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 are not related in a simple way. whole: -0.21 (0.26), residues: 1042 helix: 0.24 (0.21), residues: 610 sheet: -1.27 (0.50), residues: 110 loop : -0.12 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 192 TYR 0.012 0.001 TYR A 101 PHE 0.010 0.001 PHE B 159 TRP 0.018 0.001 TRP A 50 HIS 0.002 0.001 HIS D 7 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8600) covalent geometry : angle 0.54143 (11698) hydrogen bonds : bond 0.05899 ( 488) hydrogen bonds : angle 5.05978 ( 1410) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7672 (tp30) REVERT: B 62 TYR cc_start: 0.6908 (m-80) cc_final: 0.6658 (m-80) REVERT: B 97 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7641 (tp30) REVERT: C 113 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7541 (mp0) REVERT: C 197 GLN cc_start: 0.7862 (mt0) cc_final: 0.7433 (mm-40) REVERT: D 100 ASP cc_start: 0.7065 (t0) cc_final: 0.6732 (t0) REVERT: D 197 GLN cc_start: 0.7767 (mt0) cc_final: 0.7418 (mm-40) outliers start: 12 outliers final: 10 residues processed: 115 average time/residue: 0.1614 time to fit residues: 27.8930 Evaluate side-chains 110 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 168 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN B 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.141747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.114432 restraints weight = 28981.451| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.02 r_work: 0.3116 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8600 Z= 0.149 Angle : 0.515 4.672 11698 Z= 0.278 Chirality : 0.039 0.140 1338 Planarity : 0.004 0.039 1454 Dihedral : 9.440 87.145 1210 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.80 % Allowed : 17.34 % Favored : 80.86 % 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 are not related in a simple way. whole: 0.05 (0.26), residues: 1042 helix: 0.57 (0.21), residues: 614 sheet: -1.29 (0.49), residues: 112 loop : -0.23 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 192 TYR 0.011 0.001 TYR B 101 PHE 0.011 0.001 PHE B 159 TRP 0.018 0.001 TRP B 50 HIS 0.002 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8600) covalent geometry : angle 0.51542 (11698) hydrogen bonds : bond 0.04892 ( 488) hydrogen bonds : angle 4.69504 ( 1410) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7829 (tppt) cc_final: 0.7358 (mttt) REVERT: A 97 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7631 (tp30) REVERT: A 214 GLN cc_start: 0.6986 (tt0) cc_final: 0.6746 (tt0) REVERT: A 293 TYR cc_start: 0.8121 (m-80) cc_final: 0.7899 (m-80) REVERT: B 97 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7651 (tp30) REVERT: B 214 GLN cc_start: 0.7233 (tt0) cc_final: 0.6859 (tt0) REVERT: B 293 TYR cc_start: 0.8151 (m-80) cc_final: 0.7908 (m-80) REVERT: C 106 ASP cc_start: 0.7829 (t0) cc_final: 0.7502 (t0) REVERT: C 128 GLN cc_start: 0.7825 (mt0) cc_final: 0.7618 (mt0) REVERT: C 197 GLN cc_start: 0.7793 (mt0) cc_final: 0.7336 (mm-40) REVERT: D 100 ASP cc_start: 0.7080 (t0) cc_final: 0.6746 (t0) REVERT: D 106 ASP cc_start: 0.7850 (t0) cc_final: 0.7560 (t0) REVERT: D 197 GLN cc_start: 0.7812 (mt0) cc_final: 0.7353 (mm-40) outliers start: 16 outliers final: 15 residues processed: 111 average time/residue: 0.1763 time to fit residues: 28.9803 Evaluate side-chains 123 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 223 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 26 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 187 ASN B 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.153083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125964 restraints weight = 29313.273| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.18 r_work: 0.3298 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8600 Z= 0.188 Angle : 0.541 4.576 11698 Z= 0.294 Chirality : 0.040 0.140 1338 Planarity : 0.004 0.040 1454 Dihedral : 9.669 84.726 1210 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.70 % Allowed : 18.02 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.07 (0.26), residues: 1042 helix: 0.48 (0.21), residues: 618 sheet: -1.02 (0.51), residues: 100 loop : -0.48 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 201 TYR 0.009 0.001 TYR B 101 PHE 0.015 0.001 PHE B 217 TRP 0.017 0.001 TRP A 50 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8600) covalent geometry : angle 0.54089 (11698) hydrogen bonds : bond 0.04808 ( 488) hydrogen bonds : angle 4.64861 ( 1410) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7878 (tppt) cc_final: 0.7414 (mttt) REVERT: A 97 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7442 (tp30) REVERT: A 163 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7559 (t) REVERT: A 214 GLN cc_start: 0.7279 (tt0) cc_final: 0.6866 (tt0) REVERT: B 92 LYS cc_start: 0.7863 (tppt) cc_final: 0.7396 (mttt) REVERT: B 97 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7431 (tp30) REVERT: B 163 VAL cc_start: 0.7839 (OUTLIER) cc_final: 0.7610 (t) REVERT: B 214 GLN cc_start: 0.7086 (tt0) cc_final: 0.6675 (tt0) REVERT: C 106 ASP cc_start: 0.7877 (t0) cc_final: 0.7546 (t0) REVERT: C 197 GLN cc_start: 0.7899 (mt0) cc_final: 0.7401 (mm-40) REVERT: D 100 ASP cc_start: 0.7072 (t0) cc_final: 0.6775 (t0) REVERT: D 106 ASP cc_start: 0.7905 (t0) cc_final: 0.7568 (t0) REVERT: D 197 GLN cc_start: 0.7910 (mt0) cc_final: 0.7407 (mm-40) outliers start: 24 outliers final: 19 residues processed: 118 average time/residue: 0.1974 time to fit residues: 33.2067 Evaluate side-chains 127 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 223 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126707 restraints weight = 29251.831| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.20 r_work: 0.3310 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8600 Z= 0.158 Angle : 0.510 4.593 11698 Z= 0.276 Chirality : 0.039 0.137 1338 Planarity : 0.004 0.040 1454 Dihedral : 9.731 87.252 1210 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.36 % Allowed : 18.47 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.15 (0.26), residues: 1042 helix: 0.73 (0.21), residues: 604 sheet: -0.84 (0.53), residues: 100 loop : -0.55 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 118 TYR 0.011 0.001 TYR B 101 PHE 0.011 0.001 PHE B 159 TRP 0.017 0.001 TRP A 50 HIS 0.004 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8600) covalent geometry : angle 0.51002 (11698) hydrogen bonds : bond 0.04484 ( 488) hydrogen bonds : angle 4.52154 ( 1410) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7905 (tppt) cc_final: 0.7429 (mttt) REVERT: A 97 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7659 (tp30) REVERT: A 163 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.7611 (t) REVERT: A 214 GLN cc_start: 0.7319 (tt0) cc_final: 0.7083 (tt0) REVERT: B 92 LYS cc_start: 0.7836 (tppt) cc_final: 0.7288 (mttt) REVERT: B 97 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7648 (tp30) REVERT: B 163 VAL cc_start: 0.7829 (OUTLIER) cc_final: 0.7583 (t) REVERT: B 214 GLN cc_start: 0.7138 (tt0) cc_final: 0.6891 (tt0) outliers start: 21 outliers final: 18 residues processed: 119 average time/residue: 0.1726 time to fit residues: 30.3368 Evaluate side-chains 129 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 223 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126128 restraints weight = 29203.498| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.17 r_work: 0.3303 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8600 Z= 0.165 Angle : 0.511 4.495 11698 Z= 0.277 Chirality : 0.039 0.137 1338 Planarity : 0.004 0.040 1454 Dihedral : 9.790 88.744 1210 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.82 % Allowed : 19.14 % Favored : 78.04 % 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 are not related in a simple way. whole: 0.18 (0.26), residues: 1042 helix: 0.76 (0.21), residues: 604 sheet: -1.03 (0.51), residues: 100 loop : -0.50 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 147 TYR 0.010 0.001 TYR B 101 PHE 0.011 0.001 PHE B 159 TRP 0.017 0.001 TRP B 50 HIS 0.004 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8600) covalent geometry : angle 0.51067 (11698) hydrogen bonds : bond 0.04446 ( 488) hydrogen bonds : angle 4.49379 ( 1410) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7813 (tppt) cc_final: 0.7265 (mttt) REVERT: A 97 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7797 (tp30) REVERT: A 163 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7735 (t) REVERT: B 92 LYS cc_start: 0.7798 (tppt) cc_final: 0.7246 (mttt) REVERT: B 97 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7636 (tp30) REVERT: B 163 VAL cc_start: 0.7859 (OUTLIER) cc_final: 0.7615 (t) REVERT: C 204 MET cc_start: 0.8625 (mmm) cc_final: 0.8213 (mmm) REVERT: D 100 ASP cc_start: 0.7034 (t0) cc_final: 0.6777 (t0) REVERT: D 204 MET cc_start: 0.8644 (mmm) cc_final: 0.8224 (mmm) outliers start: 25 outliers final: 23 residues processed: 120 average time/residue: 0.1699 time to fit residues: 29.9931 Evaluate side-chains 132 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 223 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127665 restraints weight = 29061.980| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.17 r_work: 0.3336 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8600 Z= 0.127 Angle : 0.488 4.543 11698 Z= 0.263 Chirality : 0.039 0.150 1338 Planarity : 0.003 0.040 1454 Dihedral : 9.595 89.019 1210 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.15 % Allowed : 19.71 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.36 (0.27), residues: 1042 helix: 0.96 (0.22), residues: 606 sheet: -0.88 (0.52), residues: 100 loop : -0.57 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 192 TYR 0.012 0.001 TYR B 101 PHE 0.008 0.001 PHE A 159 TRP 0.016 0.001 TRP B 50 HIS 0.003 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8600) covalent geometry : angle 0.48754 (11698) hydrogen bonds : bond 0.04180 ( 488) hydrogen bonds : angle 4.38745 ( 1410) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7802 (tppt) cc_final: 0.7267 (mttt) REVERT: A 163 VAL cc_start: 0.7811 (OUTLIER) cc_final: 0.7558 (t) REVERT: B 92 LYS cc_start: 0.7799 (tppt) cc_final: 0.7256 (mttt) REVERT: B 163 VAL cc_start: 0.7845 (OUTLIER) cc_final: 0.7598 (t) REVERT: C 204 MET cc_start: 0.8622 (mmm) cc_final: 0.8202 (mmm) REVERT: D 100 ASP cc_start: 0.7040 (t0) cc_final: 0.6784 (t0) outliers start: 28 outliers final: 22 residues processed: 126 average time/residue: 0.1688 time to fit residues: 31.6562 Evaluate side-chains 129 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 223 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 72 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 103 optimal weight: 0.3980 chunk 18 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.154918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127554 restraints weight = 29250.915| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.22 r_work: 0.3329 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8600 Z= 0.128 Angle : 0.485 4.522 11698 Z= 0.262 Chirality : 0.039 0.155 1338 Planarity : 0.003 0.041 1454 Dihedral : 9.357 83.174 1210 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.70 % Allowed : 20.16 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.27), residues: 1042 helix: 1.01 (0.22), residues: 606 sheet: -0.94 (0.52), residues: 100 loop : -0.50 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 147 TYR 0.011 0.001 TYR B 101 PHE 0.008 0.001 PHE B 159 TRP 0.016 0.001 TRP B 50 HIS 0.003 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8600) covalent geometry : angle 0.48525 (11698) hydrogen bonds : bond 0.04091 ( 488) hydrogen bonds : angle 4.33139 ( 1410) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7808 (tppt) cc_final: 0.7246 (mttt) REVERT: A 163 VAL cc_start: 0.7824 (OUTLIER) cc_final: 0.7562 (t) REVERT: B 92 LYS cc_start: 0.7803 (tppt) cc_final: 0.7249 (mttt) REVERT: B 163 VAL cc_start: 0.7852 (OUTLIER) cc_final: 0.7599 (t) REVERT: C 204 MET cc_start: 0.8626 (mmm) cc_final: 0.8179 (mmm) REVERT: D 100 ASP cc_start: 0.7058 (t0) cc_final: 0.6786 (t0) outliers start: 24 outliers final: 22 residues processed: 120 average time/residue: 0.1646 time to fit residues: 29.2439 Evaluate side-chains 131 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 223 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.154608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127222 restraints weight = 29088.170| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.22 r_work: 0.3314 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8600 Z= 0.141 Angle : 0.495 4.463 11698 Z= 0.267 Chirality : 0.039 0.165 1338 Planarity : 0.003 0.041 1454 Dihedral : 9.112 78.183 1210 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.70 % Allowed : 20.50 % Favored : 76.80 % 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 are not related in a simple way. whole: 0.49 (0.27), residues: 1042 helix: 1.13 (0.22), residues: 594 sheet: -1.16 (0.50), residues: 104 loop : -0.46 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 288 TYR 0.010 0.001 TYR A 101 PHE 0.009 0.001 PHE A 217 TRP 0.016 0.001 TRP A 50 HIS 0.003 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8600) covalent geometry : angle 0.49535 (11698) hydrogen bonds : bond 0.04128 ( 488) hydrogen bonds : angle 4.34476 ( 1410) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7744 (tppt) cc_final: 0.7317 (mttt) REVERT: A 163 VAL cc_start: 0.7884 (OUTLIER) cc_final: 0.7625 (t) REVERT: B 92 LYS cc_start: 0.7813 (tppt) cc_final: 0.7260 (mttt) REVERT: B 163 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7645 (t) REVERT: B 214 GLN cc_start: 0.7238 (tt0) cc_final: 0.7022 (tt0) REVERT: C 187 PHE cc_start: 0.7768 (t80) cc_final: 0.7520 (t80) REVERT: C 204 MET cc_start: 0.8624 (mmm) cc_final: 0.8171 (mmm) REVERT: D 100 ASP cc_start: 0.7055 (t0) cc_final: 0.6772 (t0) outliers start: 24 outliers final: 22 residues processed: 125 average time/residue: 0.1676 time to fit residues: 31.0624 Evaluate side-chains 135 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 223 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127537 restraints weight = 29086.521| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.17 r_work: 0.3324 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8600 Z= 0.136 Angle : 0.494 4.482 11698 Z= 0.266 Chirality : 0.039 0.173 1338 Planarity : 0.003 0.040 1454 Dihedral : 8.971 76.558 1210 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.70 % Allowed : 20.50 % Favored : 76.80 % 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 are not related in a simple way. whole: 0.53 (0.27), residues: 1042 helix: 1.17 (0.22), residues: 594 sheet: -1.13 (0.51), residues: 104 loop : -0.47 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 147 TYR 0.011 0.001 TYR A 101 PHE 0.008 0.001 PHE A 159 TRP 0.016 0.001 TRP B 50 HIS 0.003 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8600) covalent geometry : angle 0.49371 (11698) hydrogen bonds : bond 0.04065 ( 488) hydrogen bonds : angle 4.32606 ( 1410) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7747 (tppt) cc_final: 0.7317 (mttt) REVERT: A 163 VAL cc_start: 0.7851 (OUTLIER) cc_final: 0.7583 (t) REVERT: A 214 GLN cc_start: 0.7325 (tt0) cc_final: 0.7099 (tt0) REVERT: B 92 LYS cc_start: 0.7815 (tppt) cc_final: 0.7263 (mttt) REVERT: B 163 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7627 (t) REVERT: B 214 GLN cc_start: 0.7174 (tt0) cc_final: 0.6950 (tt0) REVERT: D 100 ASP cc_start: 0.7020 (t0) cc_final: 0.6753 (t0) outliers start: 24 outliers final: 22 residues processed: 122 average time/residue: 0.1669 time to fit residues: 30.4778 Evaluate side-chains 135 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 190 TRP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 190 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 223 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 18 optimal weight: 0.0040 chunk 13 optimal weight: 0.0970 chunk 56 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.159800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.132175 restraints weight = 28886.286| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.24 r_work: 0.3366 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8600 Z= 0.102 Angle : 0.467 4.622 11698 Z= 0.250 Chirality : 0.039 0.164 1338 Planarity : 0.003 0.041 1454 Dihedral : 8.549 76.353 1210 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.36 % Allowed : 20.83 % Favored : 76.80 % 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 are not related in a simple way. whole: 0.76 (0.27), residues: 1042 helix: 1.33 (0.22), residues: 594 sheet: -1.10 (0.51), residues: 106 loop : -0.29 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 217 TYR 0.013 0.001 TYR A 101 PHE 0.006 0.001 PHE A 217 TRP 0.018 0.001 TRP A 50 HIS 0.002 0.000 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 8600) covalent geometry : angle 0.46667 (11698) hydrogen bonds : bond 0.03737 ( 488) hydrogen bonds : angle 4.17077 ( 1410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3867.74 seconds wall clock time: 66 minutes 14.74 seconds (3974.74 seconds total)