Starting phenix.real_space_refine on Fri Jul 3 17:28:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z7i_14533/07_2026/7z7i_14533.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z7i_14533/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7z7i_14533/07_2026/7z7i_14533.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z7i_14533/07_2026/7z7i_14533.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z7i_14533/07_2026/7z7i_14533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z7i_14533/07_2026/7z7i_14533.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z7i_14533/07_2026/7z7i_14533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z7i_14533/07_2026/7z7i_14533.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 chiralities: 1 Restraints were copied for chains: B, E, C, A Time building chain proxies: 2.97, per 1000 atoms: 0.20 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: 1.35 Conformation dependent library (CDL) restraints added in 778.7 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: 0.56 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: 2.68 Time building geometry restraints manager: 1.74 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: 8446 18.64 - 37.28: 409 37.28 - 55.92: 75 55.92 - 74.55: 50 74.55 - 93.19: 30 Dihedral angle restraints: 9010 sinusoidal: 3650 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 9007 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: 0.05 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 14.800 Find NCS groups from input model: 0.150 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 : 14.346 93.192 5580 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/Z covalent geometry : bond 0.01426 / 0.70 (15150) covalent geometry : angle 1.07755 / 0.53 (20595) hydrogen bonds : bond 0.27353 / 18.36 ( 595) hydrogen bonds : angle 8.70616 / 6.14 ( 1395) Misc. bond : bond 0.00112 / 0.05 ( 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 : 0.611 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: 0.1172 time to fit residues: 33.9520 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 : 0.593 ------------------------------------------------------------------------------- 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: 0.0170 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 115 ASN D 162 ASN B 115 ASN E 115 ASN E 162 ASN C 115 ASN C 162 ASN A 115 ASN A 162 ASN A 371 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.067193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.054989 restraints weight = 52683.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.057138 restraints weight = 28483.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.058632 restraints weight = 18738.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.059668 restraints weight = 13836.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060422 restraints weight = 11020.073| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 15155 Z= 0.214 Angle : 0.723 7.287 20595 Z= 0.363 Chirality : 0.048 0.152 2290 Planarity : 0.005 0.042 2600 Dihedral : 8.089 77.366 2100 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.53 % Allowed : 6.96 % Favored : 91.50 % 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: -1.35 (0.18), residues: 1830 helix: -1.26 (0.18), residues: 705 sheet: -0.59 (0.31), residues: 280 loop : -0.47 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 28 TYR 0.016 0.002 TYR B 294 PHE 0.023 0.002 PHE A 124 TRP 0.015 0.002 TRP C 356 HIS 0.005 0.001 HIS E 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (15150) covalent geometry : angle 0.72282 / 0.36 (20595) hydrogen bonds : bond 0.05136 / 3.45 ( 595) hydrogen bonds : angle 5.25166 / 3.71 ( 1395) Misc. bond : bond 0.00114 / 0.06 ( 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 145 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 269 MET cc_start: 0.7852 (tpp) cc_final: 0.7208 (ttp) REVERT: D 355 MET cc_start: 0.8874 (mmm) cc_final: 0.8608 (mmm) REVERT: B 176 MET cc_start: 0.7634 (mmt) cc_final: 0.7294 (mmt) REVERT: B 355 MET cc_start: 0.8986 (mmm) cc_final: 0.8713 (mmm) REVERT: E 190 MET cc_start: 0.7433 (mmm) cc_final: 0.7185 (mmt) REVERT: E 355 MET cc_start: 0.8010 (mmm) cc_final: 0.6770 (mtm) REVERT: C 165 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8279 (tp) REVERT: C 187 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: C 227 MET cc_start: 0.8846 (mmm) cc_final: 0.8450 (mpp) REVERT: C 355 MET cc_start: 0.8720 (mmm) cc_final: 0.8380 (mpp) REVERT: A 82 MET cc_start: 0.8990 (tpt) cc_final: 0.8357 (tpp) REVERT: A 269 MET cc_start: 0.7718 (mmp) cc_final: 0.7029 (tpp) REVERT: A 355 MET cc_start: 0.8001 (mpp) cc_final: 0.7624 (mpp) outliers start: 24 outliers final: 7 residues processed: 132 average time/residue: 0.1048 time to fit residues: 22.2382 Evaluate side-chains 107 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 260 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 10 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 128 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 128 ASN A 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.064956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.052843 restraints weight = 53410.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.054920 restraints weight = 28690.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.056371 restraints weight = 18908.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057378 restraints weight = 14049.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.058039 restraints weight = 11247.144| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15155 Z= 0.227 Angle : 0.686 6.443 20595 Z= 0.340 Chirality : 0.047 0.168 2290 Planarity : 0.005 0.045 2600 Dihedral : 7.541 79.119 2100 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.47 % Allowed : 8.69 % Favored : 89.84 % 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: -0.95 (0.19), residues: 1830 helix: -0.79 (0.19), residues: 700 sheet: -0.65 (0.31), residues: 315 loop : -0.25 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 147 TYR 0.012 0.002 TYR B 240 PHE 0.014 0.002 PHE C 124 TRP 0.016 0.002 TRP D 79 HIS 0.006 0.001 HIS C 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.23 (15150) covalent geometry : angle 0.68562 / 0.34 (20595) hydrogen bonds : bond 0.04992 / 3.35 ( 595) hydrogen bonds : angle 4.98347 / 3.52 ( 1395) Misc. bond : bond 0.00034 / 0.02 ( 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 124 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 47 MET cc_start: 0.8079 (ptm) cc_final: 0.7025 (ppp) REVERT: D 269 MET cc_start: 0.7918 (tpp) cc_final: 0.7470 (mtt) REVERT: D 355 MET cc_start: 0.8894 (mmm) cc_final: 0.8587 (mmm) REVERT: B 176 MET cc_start: 0.7739 (mmt) cc_final: 0.7335 (mpp) REVERT: B 269 MET cc_start: 0.8006 (tpp) cc_final: 0.7779 (tpp) REVERT: B 355 MET cc_start: 0.8966 (mmm) cc_final: 0.8720 (mmm) REVERT: E 47 MET cc_start: 0.6939 (pmm) cc_final: 0.5691 (ttt) REVERT: E 190 MET cc_start: 0.7592 (mmm) cc_final: 0.7259 (mmm) REVERT: E 355 MET cc_start: 0.8152 (mmm) cc_final: 0.7210 (mtm) REVERT: C 44 MET cc_start: 0.8524 (mmm) cc_final: 0.8090 (mmm) REVERT: C 165 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8180 (tp) REVERT: C 187 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8178 (m-30) REVERT: C 355 MET cc_start: 0.8689 (mmm) cc_final: 0.8336 (mmm) REVERT: A 269 MET cc_start: 0.8266 (mmp) cc_final: 0.7640 (tpp) outliers start: 23 outliers final: 15 residues processed: 119 average time/residue: 0.0944 time to fit residues: 18.7744 Evaluate side-chains 117 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 54 VAL Chi-restraints excluded: chain B residue 162 ASN 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 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 165 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 345 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 141 optimal weight: 0.0570 chunk 94 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 115 ASN E 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.067642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.055461 restraints weight = 52346.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.057641 restraints weight = 27793.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.059161 restraints weight = 18181.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060216 restraints weight = 13338.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.060972 restraints weight = 10584.298| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4097 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= 0.093 Angle : 0.561 7.166 20595 Z= 0.268 Chirality : 0.042 0.136 2290 Planarity : 0.004 0.038 2600 Dihedral : 6.733 68.382 2100 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.21 % Allowed : 9.52 % Favored : 89.27 % 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: -0.28 (0.20), residues: 1830 helix: -0.14 (0.20), residues: 700 sheet: -0.17 (0.29), residues: 310 loop : -0.01 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 28 TYR 0.010 0.001 TYR A 240 PHE 0.014 0.001 PHE B 223 TRP 0.012 0.001 TRP D 79 HIS 0.003 0.000 HIS C 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (15150) covalent geometry : angle 0.56082 / 0.27 (20595) hydrogen bonds : bond 0.02918 / 1.95 ( 595) hydrogen bonds : angle 4.31471 / 3.09 ( 1395) Misc. bond : bond 0.00020 / 0.01 ( 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 133 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 227 MET cc_start: 0.8803 (ttm) cc_final: 0.8552 (ttm) REVERT: D 355 MET cc_start: 0.8828 (mmm) cc_final: 0.8515 (mmm) REVERT: B 355 MET cc_start: 0.8755 (mmm) cc_final: 0.8470 (mmm) REVERT: E 47 MET cc_start: 0.6809 (pmm) cc_final: 0.5656 (ttt) REVERT: E 190 MET cc_start: 0.7588 (mmm) cc_final: 0.7318 (mmm) REVERT: E 355 MET cc_start: 0.7929 (mmm) cc_final: 0.7127 (mtm) REVERT: C 187 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: A 161 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7726 (p90) REVERT: A 269 MET cc_start: 0.8053 (mmp) cc_final: 0.7397 (tpp) outliers start: 19 outliers final: 7 residues processed: 130 average time/residue: 0.1008 time to fit residues: 21.2164 Evaluate side-chains 111 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 161 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.064745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.052574 restraints weight = 53017.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.054661 restraints weight = 28332.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.056117 restraints weight = 18625.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.057135 restraints weight = 13824.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.057869 restraints weight = 11051.867| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4337 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= 0.219 Angle : 0.661 9.519 20595 Z= 0.320 Chirality : 0.046 0.162 2290 Planarity : 0.004 0.044 2600 Dihedral : 6.968 74.665 2100 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.66 % Allowed : 10.61 % 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: -0.43 (0.20), residues: 1830 helix: -0.22 (0.20), residues: 700 sheet: -0.37 (0.28), residues: 345 loop : -0.07 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 177 TYR 0.012 0.001 TYR B 240 PHE 0.012 0.001 PHE C 21 TRP 0.014 0.002 TRP A 79 HIS 0.003 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (15150) covalent geometry : angle 0.66073 / 0.32 (20595) hydrogen bonds : bond 0.04510 / 3.04 ( 595) hydrogen bonds : angle 4.68100 / 3.31 ( 1395) Misc. bond : bond 0.00029 / 0.01 ( 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 126 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.613 Fit side-chains REVERT: D 227 MET cc_start: 0.8831 (ttm) cc_final: 0.8589 (ttm) REVERT: D 355 MET cc_start: 0.8892 (mmm) cc_final: 0.8658 (mmm) REVERT: B 187 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: B 355 MET cc_start: 0.8914 (mmm) cc_final: 0.8604 (mmm) REVERT: E 44 MET cc_start: 0.5666 (tpt) cc_final: 0.5297 (tpt) REVERT: E 47 MET cc_start: 0.6827 (pmm) cc_final: 0.5814 (ttt) REVERT: E 190 MET cc_start: 0.7563 (mmm) cc_final: 0.7256 (mmm) REVERT: E 269 MET cc_start: 0.7382 (mmm) cc_final: 0.6957 (mtt) REVERT: E 355 MET cc_start: 0.8059 (mmm) cc_final: 0.7347 (mtm) REVERT: C 47 MET cc_start: 0.7504 (mtp) cc_final: 0.7127 (mtp) outliers start: 26 outliers final: 20 residues processed: 122 average time/residue: 0.0948 time to fit residues: 19.3660 Evaluate side-chains 117 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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 250 ILE Chi-restraints excluded: chain E residue 303 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 171 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 59 optimal weight: 0.0770 chunk 136 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN C 115 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.067648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.055516 restraints weight = 51766.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.057702 restraints weight = 27569.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.059225 restraints weight = 18012.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.060277 restraints weight = 13214.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.061034 restraints weight = 10494.799| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15155 Z= 0.084 Angle : 0.552 10.019 20595 Z= 0.258 Chirality : 0.042 0.135 2290 Planarity : 0.004 0.044 2600 Dihedral : 6.337 63.378 2100 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.02 % Allowed : 10.86 % Favored : 88.12 % 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: -0.00 (0.20), residues: 1830 helix: 0.18 (0.20), residues: 705 sheet: -0.10 (0.29), residues: 300 loop : 0.08 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 183 TYR 0.009 0.001 TYR E 218 PHE 0.010 0.001 PHE B 223 TRP 0.012 0.001 TRP D 79 HIS 0.004 0.000 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.08 (15150) covalent geometry : angle 0.55157 / 0.26 (20595) hydrogen bonds : bond 0.02567 / 1.73 ( 595) hydrogen bonds : angle 4.16088 / 2.98 ( 1395) Misc. bond : bond 0.00040 / 0.02 ( 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 119 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: B 355 MET cc_start: 0.8671 (mmm) cc_final: 0.8376 (mmm) REVERT: E 47 MET cc_start: 0.6732 (pmm) cc_final: 0.5735 (ttt) REVERT: E 269 MET cc_start: 0.7015 (mmm) cc_final: 0.6535 (mtt) REVERT: E 355 MET cc_start: 0.7861 (mmm) cc_final: 0.7423 (mtm) REVERT: C 47 MET cc_start: 0.7524 (mtp) cc_final: 0.7078 (mtp) REVERT: A 161 HIS cc_start: 0.8019 (OUTLIER) cc_final: 0.7748 (p90) REVERT: A 269 MET cc_start: 0.8040 (mmp) cc_final: 0.7587 (tpp) outliers start: 16 outliers final: 12 residues processed: 115 average time/residue: 0.0946 time to fit residues: 18.1041 Evaluate side-chains 113 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 374 CYS 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 132 MET Chi-restraints excluded: chain A residue 161 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 48 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN C 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.066402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.054220 restraints weight = 52154.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.056347 restraints weight = 28033.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.057849 restraints weight = 18491.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.058898 restraints weight = 13621.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.059646 restraints weight = 10832.896| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4620 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= 0.125 Angle : 0.567 8.306 20595 Z= 0.267 Chirality : 0.043 0.134 2290 Planarity : 0.004 0.043 2600 Dihedral : 6.285 65.796 2100 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.15 % Allowed : 11.05 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.20), residues: 1830 helix: 0.23 (0.20), residues: 705 sheet: -0.03 (0.29), residues: 300 loop : -0.01 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 177 TYR 0.008 0.001 TYR E 218 PHE 0.010 0.001 PHE B 223 TRP 0.010 0.001 TRP D 79 HIS 0.003 0.000 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (15150) covalent geometry : angle 0.56749 / 0.27 (20595) hydrogen bonds : bond 0.03200 / 2.16 ( 595) hydrogen bonds : angle 4.18238 / 2.97 ( 1395) Misc. bond : bond 0.00018 / 0.01 ( 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 117 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: B 355 MET cc_start: 0.8729 (mmm) cc_final: 0.8413 (mmm) REVERT: E 47 MET cc_start: 0.6772 (pmm) cc_final: 0.5854 (ttt) REVERT: E 269 MET cc_start: 0.7075 (mmm) cc_final: 0.6637 (mtt) REVERT: E 355 MET cc_start: 0.7855 (mmm) cc_final: 0.7365 (mtm) REVERT: C 47 MET cc_start: 0.7507 (mtp) cc_final: 0.7028 (mtp) REVERT: A 82 MET cc_start: 0.9042 (tpt) cc_final: 0.8836 (tpp) outliers start: 18 outliers final: 15 residues processed: 111 average time/residue: 0.0888 time to fit residues: 16.3976 Evaluate side-chains 113 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 299 MET 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 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 132 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 128 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.064226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.052151 restraints weight = 53067.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054200 restraints weight = 28678.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.055634 restraints weight = 19031.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.056640 restraints weight = 14128.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057350 restraints weight = 11317.024| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 15155 Z= 0.242 Angle : 0.677 11.668 20595 Z= 0.326 Chirality : 0.046 0.169 2290 Planarity : 0.004 0.048 2600 Dihedral : 6.857 75.097 2100 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.53 % Allowed : 10.86 % Favored : 87.60 % 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: -0.29 (0.20), residues: 1830 helix: 0.03 (0.20), residues: 695 sheet: -0.36 (0.28), residues: 345 loop : -0.11 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 206 TYR 0.012 0.001 TYR A 306 PHE 0.013 0.002 PHE C 21 TRP 0.014 0.002 TRP E 79 HIS 0.004 0.001 HIS E 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (15150) covalent geometry : angle 0.67702 / 0.33 (20595) hydrogen bonds : bond 0.04569 / 3.07 ( 595) hydrogen bonds : angle 4.64329 / 3.29 ( 1395) Misc. bond : bond 0.00019 / 0.01 ( 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 122 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 187 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8303 (m-30) REVERT: E 47 MET cc_start: 0.6797 (pmm) cc_final: 0.6010 (ttt) REVERT: E 190 MET cc_start: 0.7552 (mmm) cc_final: 0.7342 (mmm) REVERT: E 269 MET cc_start: 0.7540 (mmm) cc_final: 0.7263 (mtt) REVERT: E 355 MET cc_start: 0.8025 (mmm) cc_final: 0.7468 (mtm) REVERT: C 47 MET cc_start: 0.7472 (mtp) cc_final: 0.6982 (mtp) REVERT: C 165 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8084 (tp) REVERT: C 269 MET cc_start: 0.8057 (tpp) cc_final: 0.7722 (mmp) REVERT: A 161 HIS cc_start: 0.8147 (OUTLIER) cc_final: 0.7853 (p90) REVERT: A 269 MET cc_start: 0.8345 (mmp) cc_final: 0.7814 (mmt) outliers start: 24 outliers final: 20 residues processed: 117 average time/residue: 0.0933 time to fit residues: 17.8642 Evaluate side-chains 120 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 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 165 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 161 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3358 r_free = 0.3358 target = 0.066855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.054681 restraints weight = 52405.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.056828 restraints weight = 27947.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058352 restraints weight = 18396.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.059406 restraints weight = 13535.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.060169 restraints weight = 10749.841| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4880 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= 0.096 Angle : 0.566 12.464 20595 Z= 0.262 Chirality : 0.042 0.134 2290 Planarity : 0.004 0.044 2600 Dihedral : 6.266 63.662 2100 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.15 % Allowed : 11.44 % Favored : 87.41 % 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: -0.02 (0.20), residues: 1830 helix: 0.30 (0.21), residues: 705 sheet: -0.12 (0.29), residues: 300 loop : -0.07 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 28 TYR 0.008 0.001 TYR E 218 PHE 0.010 0.001 PHE D 223 TRP 0.012 0.002 TRP D 79 HIS 0.004 0.000 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (15150) covalent geometry : angle 0.56569 / 0.26 (20595) hydrogen bonds : bond 0.02743 / 1.84 ( 595) hydrogen bonds : angle 4.12605 / 2.94 ( 1395) Misc. bond : bond 0.00023 / 0.01 ( 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 118 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: B 187 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8288 (m-30) REVERT: E 47 MET cc_start: 0.6814 (pmm) cc_final: 0.6013 (ttt) REVERT: E 269 MET cc_start: 0.7162 (mmm) cc_final: 0.6777 (mtt) REVERT: E 355 MET cc_start: 0.7850 (mmm) cc_final: 0.7367 (mtm) REVERT: C 47 MET cc_start: 0.7373 (mtp) cc_final: 0.6854 (mtp) REVERT: A 161 HIS cc_start: 0.8091 (OUTLIER) cc_final: 0.7838 (p90) outliers start: 18 outliers final: 15 residues processed: 114 average time/residue: 0.0772 time to fit residues: 14.8834 Evaluate side-chains 115 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 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 299 MET 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 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 A residue 132 MET Chi-restraints excluded: chain A residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 142 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 181 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 174 optimal weight: 0.0040 chunk 49 optimal weight: 8.9990 chunk 10 optimal weight: 0.0770 chunk 139 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.068161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.056041 restraints weight = 51680.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.058248 restraints weight = 27520.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.059769 restraints weight = 17925.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.060849 restraints weight = 13136.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.061620 restraints weight = 10363.044| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5041 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= 0.080 Angle : 0.552 12.346 20595 Z= 0.251 Chirality : 0.041 0.131 2290 Planarity : 0.004 0.042 2600 Dihedral : 5.750 61.144 2100 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.83 % Allowed : 11.63 % Favored : 87.54 % 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: 0.19 (0.20), residues: 1830 helix: 0.43 (0.21), residues: 710 sheet: -0.04 (0.29), residues: 300 loop : 0.10 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 312 TYR 0.009 0.001 TYR C 69 PHE 0.009 0.001 PHE B 223 TRP 0.012 0.001 TRP E 356 HIS 0.004 0.000 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.08 (15150) covalent geometry : angle 0.55192 / 0.25 (20595) hydrogen bonds : bond 0.02267 / 1.54 ( 595) hydrogen bonds : angle 3.98454 / 2.84 ( 1395) Misc. bond : bond 0.00023 / 0.01 ( 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 119 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.610 Fit side-chains REVERT: E 47 MET cc_start: 0.6619 (pmm) cc_final: 0.6058 (ttt) REVERT: E 269 MET cc_start: 0.6770 (mmm) cc_final: 0.6450 (mtt) REVERT: E 355 MET cc_start: 0.7792 (mmm) cc_final: 0.7360 (mtm) REVERT: C 47 MET cc_start: 0.7155 (mtp) cc_final: 0.6893 (mtp) REVERT: A 161 HIS cc_start: 0.8118 (OUTLIER) cc_final: 0.7862 (p90) REVERT: A 176 MET cc_start: 0.8292 (tpp) cc_final: 0.7832 (tpp) REVERT: A 269 MET cc_start: 0.8035 (mmp) cc_final: 0.7424 (tpp) outliers start: 13 outliers final: 11 residues processed: 116 average time/residue: 0.0870 time to fit residues: 16.8534 Evaluate side-chains 111 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 65 LEU 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 A residue 132 MET Chi-restraints excluded: chain A residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 130 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 133 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.066318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054198 restraints weight = 51930.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.056318 restraints weight = 27973.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.057779 restraints weight = 18452.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.058827 restraints weight = 13674.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.059486 restraints weight = 10883.477| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15155 Z= 0.130 Angle : 0.584 9.659 20595 Z= 0.271 Chirality : 0.043 0.133 2290 Planarity : 0.004 0.046 2600 Dihedral : 5.854 62.855 2100 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.09 % Allowed : 11.69 % Favored : 87.22 % 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: 0.14 (0.20), residues: 1830 helix: 0.45 (0.21), residues: 705 sheet: -0.02 (0.29), residues: 300 loop : -0.00 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.008 0.001 TYR E 218 PHE 0.010 0.001 PHE B 223 TRP 0.011 0.001 TRP C 356 HIS 0.003 0.000 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (15150) covalent geometry : angle 0.58398 / 0.27 (20595) hydrogen bonds : bond 0.03154 / 2.13 ( 595) hydrogen bonds : angle 4.09869 / 2.92 ( 1395) Misc. bond : bond 0.00012 / 0.01 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2122.03 seconds wall clock time: 37 minutes 40.59 seconds (2260.59 seconds total)