Starting phenix.real_space_refine on Fri Aug 22 22:11:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z3q_39751/08_2025/8z3q_39751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z3q_39751/08_2025/8z3q_39751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z3q_39751/08_2025/8z3q_39751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z3q_39751/08_2025/8z3q_39751.map" model { file = "/net/cci-nas-00/data/ceres_data/8z3q_39751/08_2025/8z3q_39751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z3q_39751/08_2025/8z3q_39751.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 48 5.16 5 C 5282 2.51 5 N 1429 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8277 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1841 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 1, 'ARG:plan': 4, 'TYR:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2462 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 355 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1710 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1909 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 11, 'TRANS': 252} Chain breaks: 3 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 6, 'GLN:plan1': 2, 'ARG:plan': 8, 'GLU:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 147 Time building chain proxies: 2.32, per 1000 atoms: 0.28 Number of scatterers: 8277 At special positions: 0 Unit cell: (89.3, 120.65, 128.25, 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 48 16.00 O 1518 8.00 N 1429 7.00 C 5282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.00 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: 0.67 Conformation dependent library (CDL) restraints added in 458.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 36.8% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.542A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.537A pdb=" N GLN A 246 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 247 " --> pdb=" O TRP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.574A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.569A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.607A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.762A pdb=" N ARG A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.619A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.141A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 48 removed outlier: 3.548A pdb=" N SER R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU R 32 " --> pdb=" O ILE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix removed outlier: 3.517A pdb=" N CYS R 36 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 69 removed outlier: 3.930A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 78 removed outlier: 4.336A pdb=" N TRP R 73 " --> pdb=" O THR R 69 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR R 76 " --> pdb=" O LEU R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 99 removed outlier: 4.018A pdb=" N ILE R 96 " --> pdb=" O LEU R 92 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE R 97 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 121 removed outlier: 3.796A pdb=" N ILE R 105 " --> pdb=" O ILE R 101 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 129 Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 180 through 188 removed outlier: 4.419A pdb=" N VAL R 186 " --> pdb=" O ASN R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 210 removed outlier: 3.956A pdb=" N GLY R 210 " --> pdb=" O ARG R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 251 Proline residue: R 239 - end of helix removed outlier: 3.903A pdb=" N ILE R 250 " --> pdb=" O SER R 246 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR R 251 " --> pdb=" O ARG R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 275 removed outlier: 3.589A pdb=" N HIS R 269 " --> pdb=" O PHE R 265 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER R 270 " --> pdb=" O SER R 266 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU R 272 " --> pdb=" O TYR R 268 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA R 273 " --> pdb=" O HIS R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 288 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 291 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224 removed outlier: 4.901A pdb=" N VAL A 234 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLY A 47 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A 253 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.707A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.901A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.759A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.757A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.227A 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: 6.656A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.667A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.020A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.653A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.672A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.618A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE S 216 " --> pdb=" O VAL S 155 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.735A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1182 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: 1.31 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1489 1.33 - 1.45: 2283 1.45 - 1.57: 4618 1.57 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 8457 Sorted by residual: bond pdb=" CA ALA B 106 " pdb=" C ALA B 106 " ideal model delta sigma weight residual 1.528 1.470 0.058 1.18e-02 7.18e+03 2.41e+01 bond pdb=" CA ALA A 7 " pdb=" C ALA A 7 " ideal model delta sigma weight residual 1.524 1.462 0.062 1.29e-02 6.01e+03 2.29e+01 bond pdb=" CA ALA A 12 " pdb=" CB ALA A 12 " ideal model delta sigma weight residual 1.534 1.474 0.060 1.45e-02 4.76e+03 1.72e+01 bond pdb=" N SER S 145 " pdb=" CA SER S 145 " ideal model delta sigma weight residual 1.459 1.413 0.046 1.16e-02 7.43e+03 1.57e+01 bond pdb=" CA ASP A 9 " pdb=" C ASP A 9 " ideal model delta sigma weight residual 1.521 1.476 0.045 1.29e-02 6.01e+03 1.24e+01 ... (remaining 8452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 11351 2.23 - 4.46: 142 4.46 - 6.69: 35 6.69 - 8.92: 6 8.92 - 11.16: 4 Bond angle restraints: 11538 Sorted by residual: angle pdb=" N ALA A 12 " pdb=" CA ALA A 12 " pdb=" C ALA A 12 " ideal model delta sigma weight residual 113.88 102.72 11.16 1.23e+00 6.61e-01 8.23e+01 angle pdb=" N ILE A 382 " pdb=" CA ILE A 382 " pdb=" C ILE A 382 " ideal model delta sigma weight residual 111.81 104.65 7.16 8.60e-01 1.35e+00 6.93e+01 angle pdb=" N LYS A 10 " pdb=" CA LYS A 10 " pdb=" C LYS A 10 " ideal model delta sigma weight residual 112.26 103.03 9.23 1.32e+00 5.74e-01 4.89e+01 angle pdb=" N ALA A 11 " pdb=" CA ALA A 11 " pdb=" C ALA A 11 " ideal model delta sigma weight residual 113.19 103.79 9.40 1.58e+00 4.01e-01 3.54e+01 angle pdb=" N GLY S 152 " pdb=" CA GLY S 152 " pdb=" C GLY S 152 " ideal model delta sigma weight residual 115.27 123.34 -8.07 1.41e+00 5.03e-01 3.27e+01 ... (remaining 11533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4370 17.78 - 35.56: 440 35.56 - 53.34: 101 53.34 - 71.12: 18 71.12 - 88.89: 3 Dihedral angle restraints: 4932 sinusoidal: 1670 harmonic: 3262 Sorted by residual: dihedral pdb=" C SER A 6 " pdb=" N SER A 6 " pdb=" CA SER A 6 " pdb=" CB SER A 6 " ideal model delta harmonic sigma weight residual -122.60 -110.39 -12.21 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASP B 258 " pdb=" CB ASP B 258 " pdb=" CG ASP B 258 " pdb=" OD1 ASP B 258 " ideal model delta sinusoidal sigma weight residual -30.00 -88.76 58.76 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 4929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1064 0.051 - 0.102: 232 0.102 - 0.153: 47 0.153 - 0.203: 6 0.203 - 0.254: 1 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA SER S 146 " pdb=" N SER S 146 " pdb=" C SER S 146 " pdb=" CB SER S 146 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ALA B 104 " pdb=" N ALA B 104 " pdb=" C ALA B 104 " pdb=" CB ALA B 104 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CA SER A 6 " pdb=" N SER A 6 " pdb=" C SER A 6 " pdb=" CB SER A 6 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 1347 not shown) Planarity restraints: 1467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 379 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.88e+00 pdb=" C CYS A 379 " 0.052 2.00e-02 2.50e+03 pdb=" O CYS A 379 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 380 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 8 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C GLU A 8 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU A 8 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP A 9 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 70 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO R 71 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO R 71 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 71 " -0.027 5.00e-02 4.00e+02 ... (remaining 1464 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 774 2.74 - 3.28: 7598 3.28 - 3.82: 13211 3.82 - 4.36: 14751 4.36 - 4.90: 26995 Nonbonded interactions: 63329 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.205 3.040 nonbonded pdb=" ND2 ASN A 50 " pdb=" OD2 ASP A 262 " model vdw 2.225 3.120 nonbonded pdb=" O SER A 261 " pdb=" OG SER A 261 " model vdw 2.262 3.040 nonbonded pdb=" NH1 ARG A 238 " pdb=" OD1 ASP B 186 " model vdw 2.268 3.120 nonbonded pdb=" O THR B 164 " pdb=" OG1 THR B 164 " model vdw 2.285 3.040 ... (remaining 63324 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.630 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:8.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8458 Z= 0.271 Angle : 0.679 11.156 11540 Z= 0.417 Chirality : 0.044 0.254 1350 Planarity : 0.004 0.048 1467 Dihedral : 15.336 88.895 2825 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.24 % Allowed : 24.23 % Favored : 74.54 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.26), residues: 1104 helix: 1.85 (0.28), residues: 384 sheet: 0.32 (0.31), residues: 294 loop : -1.17 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.019 0.001 TYR R 66 PHE 0.013 0.001 PHE R 95 TRP 0.010 0.001 TRP A 244 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8457) covalent geometry : angle 0.67759 (11538) SS BOND : bond 0.03367 ( 1) SS BOND : angle 3.17413 ( 2) hydrogen bonds : bond 0.20818 ( 413) hydrogen bonds : angle 6.59540 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.7869 (p) REVERT: A 381 ASP cc_start: 0.8187 (t0) cc_final: 0.7853 (t0) REVERT: B 325 MET cc_start: 0.8306 (mmt) cc_final: 0.8099 (mtp) REVERT: S 93 MET cc_start: 0.8514 (ttp) cc_final: 0.8193 (ttp) REVERT: R 32 LEU cc_start: 0.8635 (mt) cc_final: 0.8429 (mm) REVERT: R 66 TYR cc_start: 0.7550 (t80) cc_final: 0.7250 (t80) REVERT: R 237 PHE cc_start: 0.8496 (m-10) cc_final: 0.8258 (m-10) outliers start: 10 outliers final: 1 residues processed: 191 average time/residue: 0.5086 time to fit residues: 103.9857 Evaluate side-chains 179 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain S residue 147 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 237 GLN B 75 GLN B 88 ASN B 110 ASN B 119 ASN B 125 ASN B 239 ASN B 259 GLN S 142 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.121728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.103180 restraints weight = 12186.912| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.89 r_work: 0.3259 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8458 Z= 0.184 Angle : 0.602 8.577 11540 Z= 0.320 Chirality : 0.044 0.137 1350 Planarity : 0.005 0.053 1467 Dihedral : 4.457 29.741 1209 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.71 % Allowed : 22.13 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.26), residues: 1104 helix: 2.02 (0.27), residues: 383 sheet: 0.43 (0.30), residues: 293 loop : -1.21 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 115 TYR 0.015 0.002 TYR R 66 PHE 0.018 0.002 PHE B 151 TRP 0.012 0.002 TRP S 47 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8457) covalent geometry : angle 0.60141 (11538) SS BOND : bond 0.00883 ( 1) SS BOND : angle 1.12252 ( 2) hydrogen bonds : bond 0.06040 ( 413) hydrogen bonds : angle 4.58632 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.295 Fit side-chains REVERT: A 221 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8133 (mtmm) REVERT: A 381 ASP cc_start: 0.8333 (t0) cc_final: 0.8103 (t0) REVERT: B 49 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7644 (mtt-85) REVERT: B 259 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7196 (mt0) REVERT: B 304 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8423 (ttm-80) REVERT: B 325 MET cc_start: 0.8556 (mmt) cc_final: 0.8298 (mtp) REVERT: S 67 ARG cc_start: 0.8648 (mtm110) cc_final: 0.8340 (mtp180) REVERT: R 65 LEU cc_start: 0.8386 (tt) cc_final: 0.8117 (mp) REVERT: R 66 TYR cc_start: 0.7743 (t80) cc_final: 0.7393 (t80) REVERT: R 129 ARG cc_start: 0.8081 (mtm110) cc_final: 0.7841 (ttm110) outliers start: 30 outliers final: 13 residues processed: 207 average time/residue: 0.5169 time to fit residues: 114.1742 Evaluate side-chains 201 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain R residue 61 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 96 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 237 GLN A 294 GLN B 75 GLN B 88 ASN B 110 ASN B 125 ASN B 230 ASN B 239 ASN B 259 GLN B 340 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.122569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104171 restraints weight = 12229.171| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.88 r_work: 0.3277 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8458 Z= 0.139 Angle : 0.538 5.934 11540 Z= 0.289 Chirality : 0.041 0.134 1350 Planarity : 0.004 0.045 1467 Dihedral : 4.217 17.079 1207 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.83 % Allowed : 22.99 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.26), residues: 1104 helix: 2.09 (0.27), residues: 385 sheet: 0.54 (0.31), residues: 275 loop : -1.21 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 18 TYR 0.013 0.001 TYR S 190 PHE 0.015 0.001 PHE B 151 TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8457) covalent geometry : angle 0.53808 (11538) SS BOND : bond 0.01095 ( 1) SS BOND : angle 1.60535 ( 2) hydrogen bonds : bond 0.05144 ( 413) hydrogen bonds : angle 4.31458 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.191 Fit side-chains REVERT: A 221 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8175 (mtmm) REVERT: B 49 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.7667 (mtt-85) REVERT: B 304 ARG cc_start: 0.8622 (ttm-80) cc_final: 0.8372 (ttm-80) REVERT: S 4 LEU cc_start: 0.8373 (mt) cc_final: 0.8167 (tp) REVERT: S 93 MET cc_start: 0.8606 (ttp) cc_final: 0.8362 (ttp) REVERT: R 65 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8180 (mp) REVERT: R 66 TYR cc_start: 0.7721 (t80) cc_final: 0.7392 (t80) outliers start: 31 outliers final: 14 residues processed: 196 average time/residue: 0.4410 time to fit residues: 92.4610 Evaluate side-chains 196 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.0670 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.0770 chunk 21 optimal weight: 0.0870 chunk 71 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 223 GLN A 294 GLN B 75 GLN B 110 ASN B 119 ASN B 125 ASN B 230 ASN B 340 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.124358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105987 restraints weight = 12490.722| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.91 r_work: 0.3309 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8458 Z= 0.104 Angle : 0.499 5.915 11540 Z= 0.266 Chirality : 0.040 0.131 1350 Planarity : 0.004 0.044 1467 Dihedral : 3.986 16.222 1207 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.21 % Allowed : 23.86 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.26), residues: 1104 helix: 2.22 (0.27), residues: 385 sheet: 0.65 (0.31), residues: 273 loop : -1.17 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 18 TYR 0.012 0.001 TYR S 190 PHE 0.010 0.001 PHE B 151 TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8457) covalent geometry : angle 0.49915 (11538) SS BOND : bond 0.00705 ( 1) SS BOND : angle 1.42253 ( 2) hydrogen bonds : bond 0.04144 ( 413) hydrogen bonds : angle 4.05283 ( 1182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: B 304 ARG cc_start: 0.8622 (ttm-80) cc_final: 0.8407 (ttm-80) REVERT: S 93 MET cc_start: 0.8611 (ttp) cc_final: 0.8356 (ttp) REVERT: S 243 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8240 (m) REVERT: R 65 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8157 (mp) REVERT: R 66 TYR cc_start: 0.7612 (t80) cc_final: 0.7227 (t80) outliers start: 26 outliers final: 12 residues processed: 194 average time/residue: 0.4287 time to fit residues: 88.8988 Evaluate side-chains 190 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 227 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN B 88 ASN B 110 ASN B 125 ASN B 230 ASN B 239 ASN B 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.122632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104279 restraints weight = 12380.496| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.90 r_work: 0.3277 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8458 Z= 0.139 Angle : 0.532 6.019 11540 Z= 0.284 Chirality : 0.041 0.133 1350 Planarity : 0.004 0.041 1467 Dihedral : 4.111 16.115 1207 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.96 % Allowed : 24.72 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.26), residues: 1104 helix: 2.25 (0.28), residues: 387 sheet: 0.64 (0.31), residues: 275 loop : -1.16 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 18 TYR 0.013 0.001 TYR A 37 PHE 0.015 0.001 PHE B 151 TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8457) covalent geometry : angle 0.53145 (11538) SS BOND : bond 0.00955 ( 1) SS BOND : angle 1.67045 ( 2) hydrogen bonds : bond 0.04941 ( 413) hydrogen bonds : angle 4.11295 ( 1182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.221 Fit side-chains REVERT: A 10 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8439 (mtpm) REVERT: B 304 ARG cc_start: 0.8633 (ttm-80) cc_final: 0.8412 (ttm-80) REVERT: S 93 MET cc_start: 0.8630 (ttp) cc_final: 0.8388 (ttp) REVERT: R 65 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8184 (mp) REVERT: R 66 TYR cc_start: 0.7740 (t80) cc_final: 0.7307 (t80) outliers start: 32 outliers final: 20 residues processed: 194 average time/residue: 0.4485 time to fit residues: 92.9410 Evaluate side-chains 201 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 45 optimal weight: 0.0070 chunk 27 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 17 optimal weight: 0.0000 chunk 66 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 223 GLN A 294 GLN B 230 ASN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.123807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.105574 restraints weight = 12229.263| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.87 r_work: 0.3300 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8458 Z= 0.113 Angle : 0.509 6.078 11540 Z= 0.271 Chirality : 0.041 0.132 1350 Planarity : 0.004 0.040 1467 Dihedral : 3.970 16.027 1207 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.46 % Allowed : 24.47 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.26), residues: 1104 helix: 2.28 (0.27), residues: 388 sheet: 0.66 (0.31), residues: 279 loop : -1.09 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 18 TYR 0.012 0.001 TYR S 190 PHE 0.012 0.001 PHE B 151 TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8457) covalent geometry : angle 0.50864 (11538) SS BOND : bond 0.00774 ( 1) SS BOND : angle 1.54895 ( 2) hydrogen bonds : bond 0.04249 ( 413) hydrogen bonds : angle 3.98400 ( 1182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.187 Fit side-chains REVERT: B 304 ARG cc_start: 0.8618 (ttm-80) cc_final: 0.8413 (ttm-80) REVERT: S 93 MET cc_start: 0.8617 (ttp) cc_final: 0.8366 (ttp) REVERT: S 243 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8248 (m) REVERT: R 65 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8159 (mp) REVERT: R 66 TYR cc_start: 0.7678 (t80) cc_final: 0.7183 (t80) outliers start: 28 outliers final: 17 residues processed: 191 average time/residue: 0.4022 time to fit residues: 82.1534 Evaluate side-chains 195 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 294 GLN B 230 ASN B 239 ASN S 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.121030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.102669 restraints weight = 12266.889| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.89 r_work: 0.3250 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8458 Z= 0.182 Angle : 0.568 6.732 11540 Z= 0.304 Chirality : 0.043 0.134 1350 Planarity : 0.004 0.038 1467 Dihedral : 4.314 16.991 1207 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.57 % Allowed : 24.10 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.26), residues: 1104 helix: 2.18 (0.28), residues: 390 sheet: 0.63 (0.30), residues: 284 loop : -1.13 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 115 TYR 0.016 0.002 TYR R 66 PHE 0.017 0.002 PHE B 151 TRP 0.013 0.002 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8457) covalent geometry : angle 0.56771 (11538) SS BOND : bond 0.01150 ( 1) SS BOND : angle 1.95717 ( 2) hydrogen bonds : bond 0.05637 ( 413) hydrogen bonds : angle 4.21809 ( 1182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.275 Fit side-chains REVERT: B 49 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7774 (mtt180) REVERT: B 304 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8416 (ttm-80) REVERT: S 67 ARG cc_start: 0.8626 (mtm110) cc_final: 0.8362 (mtp180) REVERT: S 93 MET cc_start: 0.8639 (ttp) cc_final: 0.8410 (ttp) REVERT: R 66 TYR cc_start: 0.7862 (t80) cc_final: 0.7350 (t80) outliers start: 37 outliers final: 24 residues processed: 195 average time/residue: 0.4598 time to fit residues: 95.8179 Evaluate side-chains 205 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 4 optimal weight: 0.0470 chunk 63 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 294 GLN B 230 ASN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.121101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.102851 restraints weight = 12199.254| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.85 r_work: 0.3261 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8458 Z= 0.165 Angle : 0.575 8.384 11540 Z= 0.302 Chirality : 0.043 0.138 1350 Planarity : 0.004 0.041 1467 Dihedral : 4.290 16.839 1207 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.96 % Allowed : 24.85 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.26), residues: 1104 helix: 2.13 (0.28), residues: 388 sheet: 0.61 (0.30), residues: 284 loop : -1.20 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 115 TYR 0.014 0.002 TYR R 66 PHE 0.016 0.002 PHE B 151 TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8457) covalent geometry : angle 0.57459 (11538) SS BOND : bond 0.01065 ( 1) SS BOND : angle 1.99623 ( 2) hydrogen bonds : bond 0.05257 ( 413) hydrogen bonds : angle 4.15229 ( 1182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.225 Fit side-chains REVERT: B 49 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7767 (mtt180) REVERT: S 67 ARG cc_start: 0.8616 (mtm110) cc_final: 0.8372 (mtp180) REVERT: S 93 MET cc_start: 0.8636 (ttp) cc_final: 0.8411 (ttp) REVERT: S 192 MET cc_start: 0.8324 (ttp) cc_final: 0.8104 (ttp) REVERT: R 66 TYR cc_start: 0.7884 (t80) cc_final: 0.7408 (t80) outliers start: 32 outliers final: 23 residues processed: 193 average time/residue: 0.4904 time to fit residues: 100.7885 Evaluate side-chains 205 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain R residue 32 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 223 GLN A 294 GLN B 230 ASN B 239 ASN B 340 ASN R 85 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.119802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.101579 restraints weight = 12243.768| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.86 r_work: 0.3238 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8458 Z= 0.202 Angle : 0.604 7.694 11540 Z= 0.321 Chirality : 0.044 0.141 1350 Planarity : 0.004 0.043 1467 Dihedral : 4.480 17.184 1207 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.71 % Allowed : 25.22 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.26), residues: 1104 helix: 2.03 (0.28), residues: 389 sheet: 0.58 (0.30), residues: 289 loop : -1.23 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 115 TYR 0.017 0.002 TYR R 66 PHE 0.019 0.002 PHE B 151 TRP 0.013 0.002 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 8457) covalent geometry : angle 0.60342 (11538) SS BOND : bond 0.01337 ( 1) SS BOND : angle 2.21620 ( 2) hydrogen bonds : bond 0.05924 ( 413) hydrogen bonds : angle 4.28325 ( 1182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.358 Fit side-chains REVERT: A 293 LYS cc_start: 0.8772 (mmtp) cc_final: 0.8557 (mttt) REVERT: B 49 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7780 (mtt180) REVERT: S 67 ARG cc_start: 0.8611 (mtm110) cc_final: 0.8370 (mtp180) REVERT: R 43 TYR cc_start: 0.7887 (t80) cc_final: 0.7677 (t80) REVERT: R 66 TYR cc_start: 0.7962 (t80) cc_final: 0.7495 (t80) outliers start: 30 outliers final: 24 residues processed: 194 average time/residue: 0.5460 time to fit residues: 112.5575 Evaluate side-chains 204 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 90 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 223 GLN A 237 GLN A 294 GLN B 230 ASN B 239 ASN B 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.120475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.102253 restraints weight = 12091.802| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.84 r_work: 0.3250 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8458 Z= 0.178 Angle : 0.590 7.611 11540 Z= 0.311 Chirality : 0.043 0.140 1350 Planarity : 0.004 0.044 1467 Dihedral : 4.418 17.346 1207 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.34 % Allowed : 25.71 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.26), residues: 1104 helix: 2.00 (0.28), residues: 390 sheet: 0.60 (0.30), residues: 300 loop : -1.27 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 115 TYR 0.014 0.002 TYR A 37 PHE 0.018 0.002 PHE B 151 TRP 0.013 0.002 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 8457) covalent geometry : angle 0.58918 (11538) SS BOND : bond 0.01140 ( 1) SS BOND : angle 2.09516 ( 2) hydrogen bonds : bond 0.05481 ( 413) hydrogen bonds : angle 4.21097 ( 1182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.292 Fit side-chains REVERT: B 49 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7768 (mtt180) REVERT: S 67 ARG cc_start: 0.8584 (mtm110) cc_final: 0.8349 (mtp180) REVERT: S 192 MET cc_start: 0.8316 (ttp) cc_final: 0.8095 (ttp) REVERT: R 43 TYR cc_start: 0.7896 (t80) cc_final: 0.7683 (t80) REVERT: R 66 TYR cc_start: 0.7975 (t80) cc_final: 0.7570 (t80) outliers start: 27 outliers final: 24 residues processed: 191 average time/residue: 0.5125 time to fit residues: 104.2733 Evaluate side-chains 205 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 223 GLN A 237 GLN A 294 GLN B 230 ASN B 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.121085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.102797 restraints weight = 12272.959| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.88 r_work: 0.3256 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8458 Z= 0.157 Angle : 0.575 7.479 11540 Z= 0.304 Chirality : 0.043 0.135 1350 Planarity : 0.004 0.044 1467 Dihedral : 4.335 17.106 1207 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.46 % Allowed : 25.96 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.26), residues: 1104 helix: 2.08 (0.28), residues: 388 sheet: 0.74 (0.30), residues: 289 loop : -1.31 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 180 TYR 0.013 0.001 TYR A 37 PHE 0.016 0.001 PHE B 151 TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8457) covalent geometry : angle 0.57427 (11538) SS BOND : bond 0.01051 ( 1) SS BOND : angle 1.99965 ( 2) hydrogen bonds : bond 0.05143 ( 413) hydrogen bonds : angle 4.15223 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3378.61 seconds wall clock time: 58 minutes 3.75 seconds (3483.75 seconds total)