Starting phenix.real_space_refine on Wed Mar 4 17:50:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z7i_14533/03_2026/7z7i_14533.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z7i_14533/03_2026/7z7i_14533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z7i_14533/03_2026/7z7i_14533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z7i_14533/03_2026/7z7i_14533.map" model { file = "/net/cci-nas-00/data/ceres_data/7z7i_14533/03_2026/7z7i_14533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z7i_14533/03_2026/7z7i_14533.cif" } resolution = 3.5 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= 0.001 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: 6 Type Number sf(0) Gaussians P 20 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9310 2.51 5 N 2495 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14815 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ADP': 1, 'APR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, E, C, A Time building chain proxies: 2.42, per 1000 atoms: 0.16 Number of scatterers: 14815 At special positions: 0 Unit cell: (101.7, 90, 201.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 20 15.00 Mg 5 11.99 O 2880 8.00 N 2495 7.00 C 9310 6.00 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 453.3 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 30 sheets defined 49.9% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.576A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP D 86 " --> pdb=" O MET D 82 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR D 91 " --> pdb=" O HIS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.734A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.233A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 removed outlier: 3.656A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 removed outlier: 4.136A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 192 " --> pdb=" O TYR D 188 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.706A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.708A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 252 through 257 removed outlier: 4.180A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 268 Proline residue: D 264 - end of helix Processing helix chain 'D' and resid 273 through 283 removed outlier: 3.758A pdb=" N ILE D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.686A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 removed outlier: 3.608A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 355 removed outlier: 6.077A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.835A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.577A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP B 86 " --> pdb=" O MET B 82 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR B 91 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.733A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.234A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 removed outlier: 3.657A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 194 removed outlier: 4.137A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 192 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.706A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.708A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 252 through 257 removed outlier: 4.181A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 268 Proline residue: B 264 - end of helix Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.759A pdb=" N ILE B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.686A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.608A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 355 removed outlier: 6.077A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.836A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.576A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP E 86 " --> pdb=" O MET E 82 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR E 91 " --> pdb=" O HIS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.733A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.234A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 144 removed outlier: 3.656A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 removed outlier: 4.136A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE E 192 " --> pdb=" O TYR E 188 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.706A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE E 212 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS E 215 " --> pdb=" O ASP E 211 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 removed outlier: 3.708A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 252 through 257 removed outlier: 4.180A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 268 Proline residue: E 264 - end of helix Processing helix chain 'E' and resid 273 through 283 removed outlier: 3.758A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.686A pdb=" N ALA E 319 " --> pdb=" O LYS E 315 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 removed outlier: 3.608A pdb=" N GLY E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 355 removed outlier: 6.077A pdb=" N THR E 351 " --> pdb=" O SER E 348 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 373 removed outlier: 3.835A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.576A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP C 86 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 91 " --> pdb=" O HIS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.734A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.233A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.657A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 removed outlier: 4.137A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 192 " --> pdb=" O TYR C 188 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.706A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.709A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 252 through 257 removed outlier: 4.181A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 268 Proline residue: C 264 - end of helix Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.757A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.686A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 removed outlier: 3.608A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 355 removed outlier: 6.076A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.836A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.576A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.734A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.234A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.656A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 removed outlier: 4.136A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 192 " --> pdb=" O TYR A 188 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.705A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.708A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 252 through 257 removed outlier: 4.181A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 268 Proline residue: A 264 - end of helix Processing helix chain 'A' and resid 273 through 283 removed outlier: 3.758A pdb=" N ILE A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.686A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.609A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 355 removed outlier: 6.077A pdb=" N THR A 351 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.836A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.578A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D 20 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 9 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.170A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.578A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 20 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 9 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 133 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.170A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.578A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY E 20 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL E 9 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR E 133 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET E 132 " --> pdb=" O ILE E 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.170A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.579A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 20 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 9 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.170A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.578A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 20 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 132 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.170A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 238 through 241 605 hydrogen bonds defined for protein. 1395 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: 2.60 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4785 1.34 - 1.46: 2649 1.46 - 1.57: 7476 1.57 - 1.69: 35 1.69 - 1.81: 205 Bond restraints: 15150 Sorted by residual: bond pdb=" C1' APR E 403 " pdb=" O4' APR E 403 " ideal model delta sigma weight residual 1.393 1.647 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C1' APR A 403 " pdb=" O4' APR A 403 " ideal model delta sigma weight residual 1.393 1.647 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C1' APR B 403 " pdb=" O4' APR B 403 " ideal model delta sigma weight residual 1.393 1.647 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C1' APR D 403 " pdb=" O4' APR D 403 " ideal model delta sigma weight residual 1.393 1.647 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C1' APR C 403 " pdb=" O4' APR C 403 " ideal model delta sigma weight residual 1.393 1.646 -0.253 2.00e-02 2.50e+03 1.60e+02 ... (remaining 15145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 20100 2.83 - 5.67: 391 5.67 - 8.50: 64 8.50 - 11.33: 35 11.33 - 14.16: 5 Bond angle restraints: 20595 Sorted by residual: angle pdb=" C1' APR D 403 " pdb=" O4' APR D 403 " pdb=" C4' APR D 403 " ideal model delta sigma weight residual 111.27 97.11 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C1' APR A 403 " pdb=" O4' APR A 403 " pdb=" C4' APR A 403 " ideal model delta sigma weight residual 111.27 97.11 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C1' APR E 403 " pdb=" O4' APR E 403 " pdb=" C4' APR E 403 " ideal model delta sigma weight residual 111.27 97.11 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C1' APR C 403 " pdb=" O4' APR C 403 " pdb=" C4' APR C 403 " ideal model delta sigma weight residual 111.27 97.11 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C1' APR B 403 " pdb=" O4' APR B 403 " pdb=" C4' APR B 403 " ideal model delta sigma weight residual 111.27 97.16 14.11 3.00e+00 1.11e-01 2.21e+01 ... (remaining 20590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.64: 8586 18.64 - 37.28: 477 37.28 - 55.92: 82 55.92 - 74.55: 50 74.55 - 93.19: 30 Dihedral angle restraints: 9225 sinusoidal: 3865 harmonic: 5360 Sorted by residual: dihedral pdb=" CA LEU E 65 " pdb=" C LEU E 65 " pdb=" N THR E 66 " pdb=" CA THR E 66 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LEU A 65 " pdb=" C LEU A 65 " pdb=" N THR A 66 " pdb=" CA THR A 66 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LEU B 65 " pdb=" C LEU B 65 " pdb=" N THR B 66 " pdb=" CA THR B 66 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 9222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 2191 0.129 - 0.258: 74 0.258 - 0.387: 5 0.387 - 0.516: 15 0.516 - 0.645: 5 Chirality restraints: 2290 Sorted by residual: chirality pdb=" C4D APR C 403 " pdb=" C3D APR C 403 " pdb=" C5D APR C 403 " pdb=" O4D APR C 403 " both_signs ideal model delta sigma weight residual False -2.49 -3.13 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C4D APR B 403 " pdb=" C3D APR B 403 " pdb=" C5D APR B 403 " pdb=" O4D APR B 403 " both_signs ideal model delta sigma weight residual False -2.49 -3.13 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C4D APR D 403 " pdb=" C3D APR D 403 " pdb=" C5D APR D 403 " pdb=" O4D APR D 403 " both_signs ideal model delta sigma weight residual False -2.49 -3.13 0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 2287 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 62 " -0.065 9.50e-02 1.11e+02 3.98e-02 9.59e+00 pdb=" NE ARG C 62 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 62 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG C 62 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG C 62 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 62 " 0.066 9.50e-02 1.11e+02 3.99e-02 9.51e+00 pdb=" NE ARG B 62 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 62 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG B 62 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG B 62 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 62 " -0.065 9.50e-02 1.11e+02 3.95e-02 9.50e+00 pdb=" NE ARG A 62 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 62 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG A 62 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 62 " 0.015 2.00e-02 2.50e+03 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 81 2.54 - 3.13: 11705 3.13 - 3.72: 19878 3.72 - 4.31: 29247 4.31 - 4.90: 47356 Nonbonded interactions: 108267 Sorted by model distance: nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 1.953 2.170 ... (remaining 108262 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: 0.04 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'B' selection = chain 'E' selection = chain 'C' selection = chain 'A' } 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 group one per residue 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: 2.260 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.470 Find NCS groups from input model: 0.120 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.014 0.254 15155 Z= 0.695 Angle : 1.078 14.164 20595 Z= 0.529 Chirality : 0.073 0.645 2290 Planarity : 0.005 0.040 2600 Dihedral : 14.644 93.192 5795 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -2.47 (0.18), residues: 1830 helix: -2.68 (0.14), residues: 650 sheet: -0.24 (0.29), residues: 315 loop : -1.18 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.052 0.008 ARG C 62 TYR 0.014 0.005 TYR A 143 PHE 0.015 0.002 PHE A 255 TRP 0.019 0.003 TRP B 86 HIS 0.004 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.01426 (15150) covalent geometry : angle 1.07755 (20595) hydrogen bonds : bond 0.27353 ( 595) hydrogen bonds : angle 8.70616 ( 1395) Misc. bond : bond 0.00112 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: D 286 ASP cc_start: 0.8559 (m-30) cc_final: 0.8276 (m-30) REVERT: D 355 MET cc_start: 0.8814 (mmm) cc_final: 0.8516 (mmm) REVERT: B 176 MET cc_start: 0.8100 (mmt) cc_final: 0.7685 (mmp) REVERT: B 355 MET cc_start: 0.8936 (mmm) cc_final: 0.8612 (mmm) REVERT: E 82 MET cc_start: 0.8690 (tpt) cc_final: 0.8392 (tpp) REVERT: E 355 MET cc_start: 0.7804 (mmm) cc_final: 0.6877 (mpp) REVERT: C 137 GLN cc_start: 0.8914 (mt0) cc_final: 0.8432 (mt0) REVERT: C 355 MET cc_start: 0.8695 (mmm) cc_final: 0.8265 (mpp) REVERT: A 82 MET cc_start: 0.9025 (tpt) cc_final: 0.8692 (tpt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1045 time to fit residues: 30.4202 Evaluate side-chains 109 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 ASN D 162 ASN B 115 ASN B 128 ASN E 115 ASN E 162 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 128 ASN C 162 ASN A 115 ASN A 162 ASN A 371 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.065867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.053685 restraints weight = 53108.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.055775 restraints weight = 28793.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.057235 restraints weight = 19090.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.058264 restraints weight = 14162.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.059002 restraints weight = 11325.744| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15155 Z= 0.275 Angle : 0.773 7.337 20595 Z= 0.391 Chirality : 0.049 0.171 2290 Planarity : 0.005 0.045 2600 Dihedral : 9.036 81.229 2315 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.79 % Allowed : 6.96 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.18), residues: 1830 helix: -1.34 (0.17), residues: 695 sheet: -0.65 (0.31), residues: 280 loop : -0.63 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 196 TYR 0.016 0.002 TYR B 294 PHE 0.019 0.002 PHE C 21 TRP 0.016 0.002 TRP D 79 HIS 0.004 0.001 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00636 (15150) covalent geometry : angle 0.77270 (20595) hydrogen bonds : bond 0.05570 ( 595) hydrogen bonds : angle 5.43318 ( 1395) Misc. bond : bond 0.00091 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: D 162 ASN cc_start: 0.8411 (m-40) cc_final: 0.8184 (m-40) REVERT: D 269 MET cc_start: 0.7928 (tpp) cc_final: 0.7474 (mtt) REVERT: D 355 MET cc_start: 0.8941 (mmm) cc_final: 0.8654 (mmm) REVERT: B 176 MET cc_start: 0.7717 (mmt) cc_final: 0.7369 (mmt) REVERT: B 227 MET cc_start: 0.8328 (ttm) cc_final: 0.8127 (tpp) REVERT: B 269 MET cc_start: 0.7849 (tpp) cc_final: 0.7559 (tpp) REVERT: B 355 MET cc_start: 0.9040 (mmm) cc_final: 0.8771 (mmm) REVERT: E 190 MET cc_start: 0.7452 (mmm) cc_final: 0.7201 (mmt) REVERT: E 355 MET cc_start: 0.8105 (mmm) cc_final: 0.6850 (mtm) REVERT: C 187 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8170 (m-30) REVERT: C 227 MET cc_start: 0.8834 (mmm) cc_final: 0.8489 (tpp) REVERT: C 355 MET cc_start: 0.8755 (mmm) cc_final: 0.8508 (mmm) REVERT: A 44 MET cc_start: 0.8709 (tpp) cc_final: 0.8504 (tpt) REVERT: A 82 MET cc_start: 0.9034 (tpt) cc_final: 0.8411 (tpp) REVERT: A 161 HIS cc_start: 0.8182 (OUTLIER) cc_final: 0.7824 (p90) REVERT: A 269 MET cc_start: 0.8009 (mmp) cc_final: 0.7198 (tpp) REVERT: A 355 MET cc_start: 0.8054 (mpp) cc_final: 0.7661 (mpp) outliers start: 28 outliers final: 12 residues processed: 134 average time/residue: 0.0998 time to fit residues: 21.5249 Evaluate side-chains 114 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 326 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 10 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 HIS C 115 ASN A 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.066457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.054299 restraints weight = 52887.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.056423 restraints weight = 28272.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057917 restraints weight = 18590.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.058954 restraints weight = 13689.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.059709 restraints weight = 10899.858| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15155 Z= 0.147 Angle : 0.614 6.357 20595 Z= 0.300 Chirality : 0.044 0.141 2290 Planarity : 0.004 0.040 2600 Dihedral : 8.117 74.425 2315 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.34 % Allowed : 8.50 % Favored : 90.16 % 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: -0.74 (0.19), residues: 1830 helix: -0.58 (0.19), residues: 700 sheet: -0.19 (0.30), residues: 310 loop : -0.33 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 28 TYR 0.010 0.001 TYR A 240 PHE 0.009 0.001 PHE C 21 TRP 0.015 0.002 TRP D 79 HIS 0.005 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00335 (15150) covalent geometry : angle 0.61354 (20595) hydrogen bonds : bond 0.04001 ( 595) hydrogen bonds : angle 4.69395 ( 1395) Misc. bond : bond 0.00021 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 47 MET cc_start: 0.8059 (ptm) cc_final: 0.7087 (ppp) REVERT: D 269 MET cc_start: 0.7874 (tpp) cc_final: 0.7398 (mtt) REVERT: D 355 MET cc_start: 0.8836 (mmm) cc_final: 0.8554 (mmm) REVERT: B 355 MET cc_start: 0.8918 (mmm) cc_final: 0.8682 (mmm) REVERT: E 47 MET cc_start: 0.6906 (pmm) cc_final: 0.5615 (ttt) REVERT: E 82 MET cc_start: 0.8957 (tpp) cc_final: 0.8728 (tpp) REVERT: E 355 MET cc_start: 0.8035 (mmm) cc_final: 0.7209 (mtm) REVERT: C 187 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8143 (m-30) REVERT: C 355 MET cc_start: 0.8623 (mmm) cc_final: 0.8257 (mmm) REVERT: A 82 MET cc_start: 0.9006 (tpt) cc_final: 0.8801 (tpp) REVERT: A 161 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7833 (p90) REVERT: A 269 MET cc_start: 0.8089 (mmp) cc_final: 0.7372 (tpp) outliers start: 21 outliers final: 11 residues processed: 122 average time/residue: 0.0901 time to fit residues: 18.4206 Evaluate side-chains 112 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain E residue 356 TRP Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain A residue 161 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 ASN C 115 ASN A 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.063837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.051675 restraints weight = 53750.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.053745 restraints weight = 29015.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.055187 restraints weight = 19217.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.056193 restraints weight = 14284.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.056904 restraints weight = 11454.903| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15155 Z= 0.273 Angle : 0.716 6.640 20595 Z= 0.355 Chirality : 0.048 0.178 2290 Planarity : 0.005 0.045 2600 Dihedral : 8.206 82.442 2315 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.17 % Allowed : 9.33 % Favored : 88.50 % 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: -0.88 (0.19), residues: 1830 helix: -0.54 (0.20), residues: 670 sheet: -0.76 (0.29), residues: 340 loop : -0.33 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.014 0.002 TYR B 166 PHE 0.014 0.002 PHE C 21 TRP 0.017 0.002 TRP D 79 HIS 0.003 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00632 (15150) covalent geometry : angle 0.71570 (20595) hydrogen bonds : bond 0.05188 ( 595) hydrogen bonds : angle 5.02454 ( 1395) Misc. bond : bond 0.00077 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: D 47 MET cc_start: 0.8176 (ptm) cc_final: 0.6919 (ppp) REVERT: D 227 MET cc_start: 0.8834 (ttm) cc_final: 0.8622 (mtp) REVERT: D 269 MET cc_start: 0.8066 (tpp) cc_final: 0.7621 (mtt) REVERT: D 355 MET cc_start: 0.8905 (mmm) cc_final: 0.8681 (mmm) REVERT: B 355 MET cc_start: 0.8991 (mmm) cc_final: 0.8728 (mmm) REVERT: E 47 MET cc_start: 0.6907 (pmm) cc_final: 0.5861 (ttt) REVERT: E 190 MET cc_start: 0.7932 (mmm) cc_final: 0.7642 (mmt) REVERT: E 269 MET cc_start: 0.7675 (mmm) cc_final: 0.7248 (mtt) REVERT: E 355 MET cc_start: 0.8208 (mmm) cc_final: 0.7328 (mtm) REVERT: C 165 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8210 (tp) REVERT: C 269 MET cc_start: 0.8206 (tpp) cc_final: 0.7882 (mmp) REVERT: C 355 MET cc_start: 0.8730 (mmm) cc_final: 0.8363 (mmm) REVERT: A 161 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7932 (p90) REVERT: A 355 MET cc_start: 0.8156 (mpp) cc_final: 0.7936 (mpp) outliers start: 34 outliers final: 23 residues processed: 123 average time/residue: 0.0904 time to fit residues: 18.5959 Evaluate side-chains 119 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 356 TRP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 94 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 176 optimal weight: 0.0870 chunk 78 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 overall best weight: 3.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.064739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.052635 restraints weight = 53305.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.054740 restraints weight = 28460.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.056196 restraints weight = 18730.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.057222 restraints weight = 13881.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.057950 restraints weight = 11078.391| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15155 Z= 0.184 Angle : 0.625 8.039 20595 Z= 0.302 Chirality : 0.045 0.156 2290 Planarity : 0.004 0.043 2600 Dihedral : 7.798 79.133 2315 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.92 % Allowed : 10.35 % Favored : 87.73 % 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: -0.66 (0.20), residues: 1830 helix: -0.29 (0.20), residues: 700 sheet: -0.73 (0.30), residues: 315 loop : -0.24 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 147 TYR 0.011 0.001 TYR A 240 PHE 0.012 0.001 PHE B 223 TRP 0.016 0.002 TRP D 79 HIS 0.003 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00426 (15150) covalent geometry : angle 0.62527 (20595) hydrogen bonds : bond 0.04052 ( 595) hydrogen bonds : angle 4.60090 ( 1395) Misc. bond : bond 0.00030 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 47 MET cc_start: 0.8099 (ptm) cc_final: 0.7539 (ppp) REVERT: D 355 MET cc_start: 0.8874 (mmm) cc_final: 0.8641 (mmm) REVERT: B 187 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8281 (m-30) REVERT: B 355 MET cc_start: 0.8914 (mmm) cc_final: 0.8604 (mmm) REVERT: E 47 MET cc_start: 0.6846 (pmm) cc_final: 0.5951 (ttt) REVERT: E 190 MET cc_start: 0.7912 (mmm) cc_final: 0.7586 (mmt) REVERT: E 269 MET cc_start: 0.7552 (mmm) cc_final: 0.7087 (mtt) REVERT: E 355 MET cc_start: 0.8106 (mmm) cc_final: 0.7447 (mtm) REVERT: C 269 MET cc_start: 0.8129 (tpp) cc_final: 0.7824 (mmp) REVERT: A 161 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7840 (p90) outliers start: 30 outliers final: 24 residues processed: 124 average time/residue: 0.0946 time to fit residues: 19.4806 Evaluate side-chains 122 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain E residue 356 TRP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 326 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 171 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 ASN C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.066607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.054501 restraints weight = 51996.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.056641 restraints weight = 27735.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.058151 restraints weight = 18226.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.059194 restraints weight = 13411.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.059949 restraints weight = 10660.959| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15155 Z= 0.098 Angle : 0.554 9.060 20595 Z= 0.260 Chirality : 0.042 0.133 2290 Planarity : 0.004 0.044 2600 Dihedral : 7.244 70.724 2315 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.73 % Allowed : 11.18 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1830 helix: 0.08 (0.20), residues: 705 sheet: -0.17 (0.29), residues: 300 loop : -0.15 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 28 TYR 0.010 0.001 TYR E 218 PHE 0.011 0.001 PHE B 223 TRP 0.014 0.002 TRP D 79 HIS 0.004 0.000 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00222 (15150) covalent geometry : angle 0.55393 (20595) hydrogen bonds : bond 0.02830 ( 595) hydrogen bonds : angle 4.20113 ( 1395) Misc. bond : bond 0.00025 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: D 47 MET cc_start: 0.7899 (ptm) cc_final: 0.7410 (ppp) REVERT: D 227 MET cc_start: 0.8817 (ttm) cc_final: 0.8577 (mtp) REVERT: B 44 MET cc_start: 0.7914 (ttp) cc_final: 0.7708 (tmm) REVERT: B 355 MET cc_start: 0.8698 (mmm) cc_final: 0.8394 (mmm) REVERT: E 47 MET cc_start: 0.6786 (pmm) cc_final: 0.5869 (ttt) REVERT: E 190 MET cc_start: 0.7910 (mmm) cc_final: 0.7591 (mmt) REVERT: E 269 MET cc_start: 0.7271 (mmm) cc_final: 0.6710 (mtt) REVERT: E 355 MET cc_start: 0.7957 (mmm) cc_final: 0.7473 (mtm) REVERT: A 44 MET cc_start: 0.8556 (mmm) cc_final: 0.8218 (tpt) REVERT: A 82 MET cc_start: 0.8972 (tpt) cc_final: 0.8666 (tpp) REVERT: A 161 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7833 (p90) outliers start: 27 outliers final: 17 residues processed: 123 average time/residue: 0.0884 time to fit residues: 18.0329 Evaluate side-chains 117 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 257 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 48 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 148 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.066141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.053966 restraints weight = 52126.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.056102 restraints weight = 27920.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.057584 restraints weight = 18394.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058623 restraints weight = 13599.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.059371 restraints weight = 10847.774| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15155 Z= 0.121 Angle : 0.571 10.315 20595 Z= 0.268 Chirality : 0.043 0.131 2290 Planarity : 0.004 0.046 2600 Dihedral : 7.145 68.755 2315 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.79 % Allowed : 11.12 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.20), residues: 1830 helix: 0.20 (0.20), residues: 705 sheet: -0.12 (0.29), residues: 300 loop : -0.15 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 177 TYR 0.010 0.001 TYR E 218 PHE 0.012 0.001 PHE B 223 TRP 0.012 0.002 TRP D 79 HIS 0.003 0.000 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00280 (15150) covalent geometry : angle 0.57108 (20595) hydrogen bonds : bond 0.03171 ( 595) hydrogen bonds : angle 4.20609 ( 1395) Misc. bond : bond 0.00042 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: D 47 MET cc_start: 0.7875 (ptm) cc_final: 0.7370 (ppp) REVERT: D 227 MET cc_start: 0.8822 (ttm) cc_final: 0.8541 (ttm) REVERT: B 44 MET cc_start: 0.7962 (ttp) cc_final: 0.7648 (tmm) REVERT: B 187 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8250 (m-30) REVERT: B 227 MET cc_start: 0.8249 (ttm) cc_final: 0.7931 (mpp) REVERT: B 355 MET cc_start: 0.8698 (mmm) cc_final: 0.8450 (mmm) REVERT: E 47 MET cc_start: 0.6764 (pmm) cc_final: 0.5896 (ttt) REVERT: E 190 MET cc_start: 0.7808 (mmm) cc_final: 0.7491 (mmt) REVERT: E 269 MET cc_start: 0.7240 (mmm) cc_final: 0.6685 (mtt) REVERT: E 355 MET cc_start: 0.7909 (mmm) cc_final: 0.7363 (mtm) REVERT: C 269 MET cc_start: 0.8014 (tpp) cc_final: 0.7685 (mmp) REVERT: A 44 MET cc_start: 0.8557 (mmm) cc_final: 0.8210 (tpt) REVERT: A 82 MET cc_start: 0.8998 (tpt) cc_final: 0.8720 (tpp) REVERT: A 161 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7884 (p90) outliers start: 28 outliers final: 21 residues processed: 121 average time/residue: 0.0946 time to fit residues: 18.9852 Evaluate side-chains 121 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 128 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 68 optimal weight: 0.1980 chunk 74 optimal weight: 10.0000 chunk 181 optimal weight: 0.7980 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.064473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.052375 restraints weight = 52802.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.054449 restraints weight = 28400.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.055905 restraints weight = 18750.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.056923 restraints weight = 13909.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.057658 restraints weight = 11125.947| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15155 Z= 0.207 Angle : 0.637 11.467 20595 Z= 0.305 Chirality : 0.045 0.161 2290 Planarity : 0.004 0.046 2600 Dihedral : 7.398 74.658 2315 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.85 % Allowed : 11.12 % Favored : 87.03 % 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: -0.33 (0.20), residues: 1830 helix: 0.09 (0.20), residues: 700 sheet: -0.37 (0.28), residues: 345 loop : -0.23 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 177 TYR 0.010 0.001 TYR B 240 PHE 0.011 0.001 PHE B 223 TRP 0.013 0.002 TRP E 79 HIS 0.003 0.001 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00481 (15150) covalent geometry : angle 0.63706 (20595) hydrogen bonds : bond 0.04176 ( 595) hydrogen bonds : angle 4.51664 ( 1395) Misc. bond : bond 0.00038 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: D 47 MET cc_start: 0.7953 (ptm) cc_final: 0.7514 (ppp) REVERT: B 44 MET cc_start: 0.7964 (ttp) cc_final: 0.7575 (tmm) REVERT: B 187 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8262 (m-30) REVERT: B 227 MET cc_start: 0.8237 (ttm) cc_final: 0.7907 (mpp) REVERT: B 355 MET cc_start: 0.8825 (mmm) cc_final: 0.8479 (mmm) REVERT: E 47 MET cc_start: 0.6847 (pmm) cc_final: 0.6078 (ttt) REVERT: E 190 MET cc_start: 0.7801 (mmm) cc_final: 0.7479 (mmt) REVERT: E 269 MET cc_start: 0.7550 (mmm) cc_final: 0.7090 (mtt) REVERT: E 355 MET cc_start: 0.8025 (mmm) cc_final: 0.7435 (mtm) REVERT: C 269 MET cc_start: 0.8188 (tpp) cc_final: 0.7891 (mmp) REVERT: A 124 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: A 161 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.7882 (p90) outliers start: 29 outliers final: 23 residues processed: 117 average time/residue: 0.0848 time to fit residues: 16.7196 Evaluate side-chains 122 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 257 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.065020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.052895 restraints weight = 52756.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.054995 restraints weight = 28276.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.056457 restraints weight = 18658.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.057492 restraints weight = 13834.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.058232 restraints weight = 11021.591| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15155 Z= 0.165 Angle : 0.607 12.143 20595 Z= 0.287 Chirality : 0.044 0.150 2290 Planarity : 0.004 0.046 2600 Dihedral : 7.300 73.060 2315 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.79 % Allowed : 11.50 % Favored : 86.71 % 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: -0.33 (0.20), residues: 1830 helix: 0.11 (0.20), residues: 700 sheet: -0.39 (0.27), residues: 345 loop : -0.25 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 177 TYR 0.009 0.001 TYR E 218 PHE 0.010 0.001 PHE B 223 TRP 0.013 0.002 TRP E 79 HIS 0.002 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00384 (15150) covalent geometry : angle 0.60738 (20595) hydrogen bonds : bond 0.03699 ( 595) hydrogen bonds : angle 4.37268 ( 1395) Misc. bond : bond 0.00031 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: D 47 MET cc_start: 0.7888 (ptm) cc_final: 0.7416 (ppp) REVERT: B 44 MET cc_start: 0.7946 (ttp) cc_final: 0.7557 (tmm) REVERT: B 187 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: B 227 MET cc_start: 0.8217 (ttm) cc_final: 0.7922 (mpp) REVERT: E 47 MET cc_start: 0.6792 (pmm) cc_final: 0.6105 (ttt) REVERT: E 190 MET cc_start: 0.7777 (mmm) cc_final: 0.7463 (mmt) REVERT: E 269 MET cc_start: 0.7508 (mmm) cc_final: 0.7056 (mtt) REVERT: E 355 MET cc_start: 0.8007 (mmm) cc_final: 0.7440 (mtm) REVERT: C 269 MET cc_start: 0.8164 (tpp) cc_final: 0.7882 (mmp) REVERT: A 124 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8242 (m-80) REVERT: A 161 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7882 (p90) REVERT: A 269 MET cc_start: 0.8292 (mmp) cc_final: 0.7722 (mmt) outliers start: 28 outliers final: 23 residues processed: 119 average time/residue: 0.0930 time to fit residues: 18.7027 Evaluate side-chains 121 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 181 optimal weight: 0.1980 chunk 1 optimal weight: 7.9990 chunk 174 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.067554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.055330 restraints weight = 51661.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.057516 restraints weight = 27601.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.059020 restraints weight = 18129.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.060097 restraints weight = 13390.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.060864 restraints weight = 10628.348| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15155 Z= 0.082 Angle : 0.546 11.280 20595 Z= 0.251 Chirality : 0.041 0.134 2290 Planarity : 0.004 0.042 2600 Dihedral : 6.830 64.066 2315 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.09 % Allowed : 12.27 % Favored : 86.65 % 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: -0.08 (0.20), residues: 1830 helix: 0.29 (0.21), residues: 705 sheet: -0.16 (0.29), residues: 300 loop : -0.14 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 28 TYR 0.009 0.001 TYR E 218 PHE 0.012 0.001 PHE D 223 TRP 0.015 0.002 TRP D 79 HIS 0.004 0.000 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00183 (15150) covalent geometry : angle 0.54559 (20595) hydrogen bonds : bond 0.02387 ( 595) hydrogen bonds : angle 4.04784 ( 1395) Misc. bond : bond 0.00033 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 355 MET cc_start: 0.8754 (mmm) cc_final: 0.8549 (mmm) REVERT: B 44 MET cc_start: 0.7901 (ttp) cc_final: 0.7566 (tmm) REVERT: B 187 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8232 (m-30) REVERT: E 47 MET cc_start: 0.6681 (pmm) cc_final: 0.6049 (ttt) REVERT: E 190 MET cc_start: 0.7756 (mmm) cc_final: 0.7468 (mmt) REVERT: E 269 MET cc_start: 0.7205 (mmm) cc_final: 0.6653 (mtt) REVERT: E 355 MET cc_start: 0.7809 (mmm) cc_final: 0.7380 (mtm) REVERT: A 44 MET cc_start: 0.8537 (mmm) cc_final: 0.8220 (tpt) REVERT: A 82 MET cc_start: 0.9010 (tpt) cc_final: 0.8703 (tpp) REVERT: A 124 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: A 161 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7837 (p90) REVERT: A 269 MET cc_start: 0.8135 (mmp) cc_final: 0.7704 (tpp) outliers start: 17 outliers final: 12 residues processed: 120 average time/residue: 0.0906 time to fit residues: 17.7698 Evaluate side-chains 117 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 130 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 79 optimal weight: 0.0170 chunk 82 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 0.0970 chunk 106 optimal weight: 6.9990 overall best weight: 2.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.065498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.053308 restraints weight = 52156.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.055408 restraints weight = 28228.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.056878 restraints weight = 18718.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.057903 restraints weight = 13898.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.058643 restraints weight = 11124.932| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15155 Z= 0.157 Angle : 0.606 10.847 20595 Z= 0.284 Chirality : 0.044 0.139 2290 Planarity : 0.004 0.044 2600 Dihedral : 6.965 66.852 2315 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.21 % Allowed : 12.27 % Favored : 86.52 % 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: -0.09 (0.20), residues: 1830 helix: 0.35 (0.20), residues: 695 sheet: -0.20 (0.28), residues: 310 loop : -0.20 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.010 0.001 TYR C 279 PHE 0.015 0.001 PHE D 223 TRP 0.012 0.002 TRP A 79 HIS 0.002 0.000 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00365 (15150) covalent geometry : angle 0.60564 (20595) hydrogen bonds : bond 0.03544 ( 595) hydrogen bonds : angle 4.25109 ( 1395) Misc. bond : bond 0.00027 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2008.49 seconds wall clock time: 35 minutes 35.70 seconds (2135.70 seconds total)