Starting phenix.real_space_refine on Fri Jun 13 18:10:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z7i_14533/06_2025/7z7i_14533.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z7i_14533/06_2025/7z7i_14533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z7i_14533/06_2025/7z7i_14533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z7i_14533/06_2025/7z7i_14533.map" model { file = "/net/cci-nas-00/data/ceres_data/7z7i_14533/06_2025/7z7i_14533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z7i_14533/06_2025/7z7i_14533.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14815 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" 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: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ADP': 1, 'APR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, E, D Time building chain proxies: 7.06, per 1000 atoms: 0.48 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: 4.05 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.92 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: 5.13 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4785 1.34 - 1.46: 2649 1.46 - 1.57: 7476 1.57 - 1.69: 35 1.69 - 1.81: 205 Bond restraints: 15150 Sorted by residual: bond pdb=" C1' APR E 403 " pdb=" O4' APR E 403 " ideal model delta sigma weight residual 1.393 1.647 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C1' APR A 403 " pdb=" O4' APR A 403 " ideal model delta sigma weight residual 1.393 1.647 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C1' APR B 403 " pdb=" O4' APR B 403 " ideal model delta sigma weight residual 1.393 1.647 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C1' APR D 403 " pdb=" O4' APR D 403 " ideal model delta sigma weight residual 1.393 1.647 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C1' APR C 403 " pdb=" O4' APR C 403 " ideal model delta sigma weight residual 1.393 1.646 -0.253 2.00e-02 2.50e+03 1.60e+02 ... (remaining 15145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 20100 2.83 - 5.67: 391 5.67 - 8.50: 64 8.50 - 11.33: 35 11.33 - 14.16: 5 Bond angle restraints: 20595 Sorted by residual: angle pdb=" C1' APR D 403 " pdb=" O4' APR D 403 " pdb=" C4' APR D 403 " ideal model delta sigma weight residual 111.27 97.11 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C1' APR A 403 " pdb=" O4' APR A 403 " pdb=" C4' APR A 403 " ideal model delta sigma weight residual 111.27 97.11 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C1' APR E 403 " pdb=" O4' APR E 403 " pdb=" C4' APR E 403 " ideal model delta sigma weight residual 111.27 97.11 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C1' APR C 403 " pdb=" O4' APR C 403 " pdb=" C4' APR C 403 " ideal model delta sigma weight residual 111.27 97.11 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C1' APR B 403 " pdb=" O4' APR B 403 " pdb=" C4' APR B 403 " ideal model delta sigma weight residual 111.27 97.16 14.11 3.00e+00 1.11e-01 2.21e+01 ... (remaining 20590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.64: 8586 18.64 - 37.28: 477 37.28 - 55.92: 82 55.92 - 74.55: 50 74.55 - 93.19: 30 Dihedral angle restraints: 9225 sinusoidal: 3865 harmonic: 5360 Sorted by residual: dihedral pdb=" CA LEU E 65 " pdb=" C LEU E 65 " pdb=" N THR E 66 " pdb=" CA THR E 66 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LEU A 65 " pdb=" C LEU A 65 " pdb=" N THR A 66 " pdb=" CA THR A 66 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LEU B 65 " pdb=" C LEU B 65 " pdb=" N THR B 66 " pdb=" CA THR B 66 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 9222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 2191 0.129 - 0.258: 74 0.258 - 0.387: 5 0.387 - 0.516: 15 0.516 - 0.645: 5 Chirality restraints: 2290 Sorted by residual: chirality pdb=" C4D APR C 403 " pdb=" C3D APR C 403 " pdb=" C5D APR C 403 " pdb=" O4D APR C 403 " both_signs ideal model delta sigma weight residual False -2.49 -3.13 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C4D APR B 403 " pdb=" C3D APR B 403 " pdb=" C5D APR B 403 " pdb=" O4D APR B 403 " both_signs ideal model delta sigma weight residual False -2.49 -3.13 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C4D APR D 403 " pdb=" C3D APR D 403 " pdb=" C5D APR D 403 " pdb=" O4D APR D 403 " both_signs ideal model delta sigma weight residual False -2.49 -3.13 0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 2287 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 62 " -0.065 9.50e-02 1.11e+02 3.98e-02 9.59e+00 pdb=" NE ARG C 62 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 62 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG C 62 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG C 62 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 62 " 0.066 9.50e-02 1.11e+02 3.99e-02 9.51e+00 pdb=" NE ARG B 62 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 62 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG B 62 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG B 62 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 62 " -0.065 9.50e-02 1.11e+02 3.95e-02 9.50e+00 pdb=" NE ARG A 62 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 62 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG A 62 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 62 " 0.015 2.00e-02 2.50e+03 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 81 2.54 - 3.13: 11705 3.13 - 3.72: 19878 3.72 - 4.31: 29247 4.31 - 4.90: 47356 Nonbonded interactions: 108267 Sorted by model distance: nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 1.953 2.170 ... (remaining 108262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.570 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.254 15155 Z= 0.695 Angle : 1.078 14.164 20595 Z= 0.529 Chirality : 0.073 0.645 2290 Planarity : 0.005 0.040 2600 Dihedral : 14.644 93.192 5795 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.003 TRP B 86 HIS 0.004 0.001 HIS C 88 PHE 0.015 0.002 PHE A 255 TYR 0.014 0.005 TYR A 143 ARG 0.052 0.008 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.27353 ( 595) hydrogen bonds : angle 8.70616 ( 1395) covalent geometry : bond 0.01426 (15150) covalent geometry : angle 1.07755 (20595) Misc. bond : bond 0.00112 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.737 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: 0.2521 time to fit residues: 72.3328 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 : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 ASN D 162 ASN B 115 ASN E 115 ASN E 162 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 162 ASN A 115 ASN A 162 ASN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.068819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056537 restraints weight = 51696.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.058719 restraints weight = 27723.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.060251 restraints weight = 18145.989| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15155 Z= 0.166 Angle : 0.681 6.988 20595 Z= 0.340 Chirality : 0.046 0.140 2290 Planarity : 0.004 0.039 2600 Dihedral : 8.873 74.072 2315 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.34 % Allowed : 6.65 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 1830 helix: -1.16 (0.18), residues: 705 sheet: -0.11 (0.32), residues: 255 loop : -0.55 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 79 HIS 0.004 0.001 HIS E 371 PHE 0.017 0.001 PHE A 124 TYR 0.014 0.001 TYR B 294 ARG 0.005 0.001 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 595) hydrogen bonds : angle 5.06500 ( 1395) covalent geometry : bond 0.00378 (15150) covalent geometry : angle 0.68082 (20595) Misc. bond : bond 0.00154 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 269 MET cc_start: 0.7719 (tpp) cc_final: 0.7012 (ttp) REVERT: D 355 MET cc_start: 0.8838 (mmm) cc_final: 0.8588 (mmm) REVERT: B 123 MET cc_start: 0.8550 (tpp) cc_final: 0.8341 (tpp) REVERT: B 269 MET cc_start: 0.7479 (tpp) cc_final: 0.7151 (tpp) REVERT: B 355 MET cc_start: 0.8992 (mmm) cc_final: 0.8587 (mmm) REVERT: E 161 HIS cc_start: 0.7553 (OUTLIER) cc_final: 0.7334 (p90) REVERT: E 190 MET cc_start: 0.7470 (mmm) cc_final: 0.7247 (mmt) REVERT: E 355 MET cc_start: 0.7902 (mmm) cc_final: 0.6625 (mtm) REVERT: C 187 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8140 (m-30) REVERT: C 227 MET cc_start: 0.8824 (mmm) cc_final: 0.8427 (mpp) REVERT: C 355 MET cc_start: 0.8707 (mmm) cc_final: 0.8354 (mpp) REVERT: A 82 MET cc_start: 0.8961 (tpt) cc_final: 0.8326 (tpp) REVERT: A 269 MET cc_start: 0.7298 (mmp) cc_final: 0.6521 (tpp) REVERT: A 355 MET cc_start: 0.8005 (mpp) cc_final: 0.7571 (mpp) outliers start: 21 outliers final: 5 residues processed: 136 average time/residue: 0.2347 time to fit residues: 50.4328 Evaluate side-chains 104 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 161 HIS Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain A residue 117 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 HIS ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.067840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.055570 restraints weight = 51571.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.057732 restraints weight = 27819.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059241 restraints weight = 18289.746| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15155 Z= 0.138 Angle : 0.600 6.341 20595 Z= 0.293 Chirality : 0.044 0.135 2290 Planarity : 0.004 0.040 2600 Dihedral : 7.983 69.865 2315 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.60 % Allowed : 8.05 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.19), residues: 1830 helix: -0.47 (0.19), residues: 705 sheet: -0.00 (0.30), residues: 310 loop : 0.01 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 79 HIS 0.009 0.001 HIS C 371 PHE 0.009 0.001 PHE C 124 TYR 0.011 0.001 TYR C 143 ARG 0.003 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 595) hydrogen bonds : angle 4.60042 ( 1395) covalent geometry : bond 0.00314 (15150) covalent geometry : angle 0.59993 (20595) Misc. bond : bond 0.00046 ( 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 135 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 355 MET cc_start: 0.8762 (mmm) cc_final: 0.8480 (mmm) REVERT: B 269 MET cc_start: 0.7699 (tpp) cc_final: 0.7398 (tpp) REVERT: B 355 MET cc_start: 0.8941 (mmm) cc_final: 0.8717 (mmm) REVERT: E 47 MET cc_start: 0.7062 (pmm) cc_final: 0.5805 (ttt) REVERT: E 355 MET cc_start: 0.7960 (mmm) cc_final: 0.6982 (mtm) REVERT: C 187 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8147 (m-30) REVERT: C 355 MET cc_start: 0.8615 (mmm) cc_final: 0.8243 (mmm) REVERT: A 82 MET cc_start: 0.8979 (tpt) cc_final: 0.8748 (tpp) REVERT: A 269 MET cc_start: 0.7782 (mmp) cc_final: 0.6897 (tpp) outliers start: 25 outliers final: 12 residues processed: 127 average time/residue: 0.2201 time to fit residues: 45.7930 Evaluate side-chains 115 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain C residue 187 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 124 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN E 115 ASN C 115 ASN C 128 ASN A 12 ASN A 115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.066099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.053879 restraints weight = 52412.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.056006 restraints weight = 28319.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057477 restraints weight = 18684.265| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15155 Z= 0.166 Angle : 0.613 6.877 20595 Z= 0.298 Chirality : 0.044 0.147 2290 Planarity : 0.004 0.040 2600 Dihedral : 7.700 70.980 2315 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.28 % Allowed : 9.58 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.20), residues: 1830 helix: -0.19 (0.20), residues: 700 sheet: -0.09 (0.29), residues: 310 loop : 0.03 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.003 0.001 HIS B 88 PHE 0.013 0.001 PHE B 223 TYR 0.011 0.001 TYR E 306 ARG 0.002 0.000 ARG C 116 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 595) hydrogen bonds : angle 4.53765 ( 1395) covalent geometry : bond 0.00383 (15150) covalent geometry : angle 0.61284 (20595) Misc. bond : bond 0.00031 ( 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 121 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 355 MET cc_start: 0.8915 (mmm) cc_final: 0.8599 (mmm) REVERT: B 355 MET cc_start: 0.8942 (mmm) cc_final: 0.8647 (mmm) REVERT: E 47 MET cc_start: 0.6829 (pmm) cc_final: 0.5772 (ttt) REVERT: E 190 MET cc_start: 0.7923 (mmm) cc_final: 0.7670 (mmt) REVERT: E 355 MET cc_start: 0.7998 (mmm) cc_final: 0.7237 (mtm) REVERT: C 44 MET cc_start: 0.8472 (mmm) cc_final: 0.7997 (mmm) REVERT: C 47 MET cc_start: 0.7585 (mtp) cc_final: 0.7235 (mtp) REVERT: C 187 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8182 (m-30) REVERT: A 269 MET cc_start: 0.8123 (mmp) cc_final: 0.7457 (tpp) outliers start: 20 outliers final: 16 residues processed: 116 average time/residue: 0.2464 time to fit residues: 46.7782 Evaluate side-chains 116 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 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 C residue 54 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 146 optimal weight: 0.0980 chunk 159 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.066665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.054435 restraints weight = 52655.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056601 restraints weight = 28070.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.058099 restraints weight = 18379.561| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4255 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= 0.126 Angle : 0.570 8.039 20595 Z= 0.271 Chirality : 0.043 0.135 2290 Planarity : 0.004 0.042 2600 Dihedral : 7.358 67.423 2315 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.85 % Allowed : 9.71 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1830 helix: 0.07 (0.20), residues: 700 sheet: -0.08 (0.29), residues: 310 loop : 0.14 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 79 HIS 0.003 0.000 HIS B 88 PHE 0.010 0.001 PHE B 223 TYR 0.010 0.001 TYR A 240 ARG 0.001 0.000 ARG E 147 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 595) hydrogen bonds : angle 4.29388 ( 1395) covalent geometry : bond 0.00290 (15150) covalent geometry : angle 0.57002 (20595) Misc. bond : bond 0.00021 ( 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 133 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 227 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8658 (mtp) REVERT: D 355 MET cc_start: 0.8888 (mmm) cc_final: 0.8686 (mmm) REVERT: B 355 MET cc_start: 0.8874 (mmm) cc_final: 0.8565 (mmm) REVERT: E 47 MET cc_start: 0.6826 (pmm) cc_final: 0.5806 (ttt) REVERT: E 190 MET cc_start: 0.7913 (mmm) cc_final: 0.7630 (mmt) REVERT: E 269 MET cc_start: 0.6954 (mmm) cc_final: 0.6485 (mtt) REVERT: E 355 MET cc_start: 0.7978 (mmm) cc_final: 0.7281 (mtm) REVERT: C 44 MET cc_start: 0.8477 (mmm) cc_final: 0.7915 (mmm) REVERT: C 47 MET cc_start: 0.7561 (mtp) cc_final: 0.7161 (mtp) REVERT: C 187 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8189 (m-30) REVERT: A 269 MET cc_start: 0.8164 (mmp) cc_final: 0.7557 (tpp) outliers start: 29 outliers final: 19 residues processed: 125 average time/residue: 0.2457 time to fit residues: 50.7310 Evaluate side-chains 123 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 299 MET 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 192 ILE 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 352 PHE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 123 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 21 optimal weight: 0.0030 chunk 127 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.065591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.053332 restraints weight = 52724.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055459 restraints weight = 28416.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.056933 restraints weight = 18799.293| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15155 Z= 0.165 Angle : 0.600 7.551 20595 Z= 0.288 Chirality : 0.044 0.149 2290 Planarity : 0.004 0.044 2600 Dihedral : 7.315 69.295 2315 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.17 % Allowed : 9.39 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1830 helix: 0.09 (0.20), residues: 700 sheet: -0.12 (0.28), residues: 310 loop : 0.04 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 79 HIS 0.003 0.001 HIS B 88 PHE 0.009 0.001 PHE C 21 TYR 0.010 0.001 TYR A 240 ARG 0.002 0.000 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 595) hydrogen bonds : angle 4.40331 ( 1395) covalent geometry : bond 0.00383 (15150) covalent geometry : angle 0.59979 (20595) Misc. bond : bond 0.00055 ( 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 137 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 1.828 Fit side-chains revert: symmetry clash REVERT: D 227 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8640 (mtp) REVERT: D 355 MET cc_start: 0.8878 (mmm) cc_final: 0.8658 (mmm) REVERT: B 187 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: B 355 MET cc_start: 0.8902 (mmm) cc_final: 0.8579 (mmm) REVERT: E 47 MET cc_start: 0.6813 (pmm) cc_final: 0.5919 (ttt) REVERT: E 190 MET cc_start: 0.7851 (mmm) cc_final: 0.7545 (mmt) REVERT: E 269 MET cc_start: 0.7347 (mmm) cc_final: 0.6911 (mtt) REVERT: E 355 MET cc_start: 0.7972 (mmm) cc_final: 0.7381 (mtm) REVERT: C 44 MET cc_start: 0.8454 (mmm) cc_final: 0.7884 (mmm) REVERT: C 47 MET cc_start: 0.7597 (mtp) cc_final: 0.7135 (mtp) REVERT: C 187 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8214 (m-30) outliers start: 34 outliers final: 24 residues processed: 129 average time/residue: 0.2091 time to fit residues: 44.5504 Evaluate side-chains 126 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 1.683 ------------------------------------------------------------------------------- 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 227 MET 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 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 103 THR 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 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 257 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 44 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.065313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053145 restraints weight = 52773.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.055279 restraints weight = 28277.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.056743 restraints weight = 18608.303| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15155 Z= 0.172 Angle : 0.606 8.209 20595 Z= 0.290 Chirality : 0.044 0.152 2290 Planarity : 0.004 0.049 2600 Dihedral : 7.281 69.339 2315 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.11 % Allowed : 10.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1830 helix: 0.12 (0.20), residues: 700 sheet: -0.16 (0.29), residues: 310 loop : -0.06 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 79 HIS 0.002 0.001 HIS B 88 PHE 0.010 0.001 PHE B 223 TYR 0.009 0.001 TYR B 240 ARG 0.002 0.000 ARG C 183 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 595) hydrogen bonds : angle 4.39350 ( 1395) covalent geometry : bond 0.00398 (15150) covalent geometry : angle 0.60610 (20595) Misc. bond : bond 0.00040 ( 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 133 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 1.719 Fit side-chains revert: symmetry clash REVERT: D 227 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8672 (mtp) REVERT: D 355 MET cc_start: 0.8872 (mmm) cc_final: 0.8626 (mmm) REVERT: B 44 MET cc_start: 0.8111 (ttp) cc_final: 0.7556 (tmm) REVERT: B 187 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8324 (m-30) REVERT: B 355 MET cc_start: 0.8871 (mmm) cc_final: 0.8519 (mmm) REVERT: E 47 MET cc_start: 0.6865 (pmm) cc_final: 0.6020 (ttt) REVERT: E 190 MET cc_start: 0.7795 (mmm) cc_final: 0.7485 (mmt) REVERT: E 269 MET cc_start: 0.7379 (mmm) cc_final: 0.6949 (mtt) REVERT: E 355 MET cc_start: 0.7973 (mmm) cc_final: 0.7337 (mtm) REVERT: C 47 MET cc_start: 0.7544 (mtp) cc_final: 0.7058 (mtp) REVERT: C 187 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8168 (m-30) REVERT: C 227 MET cc_start: 0.8772 (mmm) cc_final: 0.8409 (tpp) REVERT: A 124 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8627 (m-80) outliers start: 33 outliers final: 28 residues processed: 126 average time/residue: 0.2176 time to fit residues: 45.3612 Evaluate side-chains 129 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 227 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 122 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.054722 restraints weight = 52084.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.056893 restraints weight = 27730.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.058393 restraints weight = 18122.327| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4751 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= 0.097 Angle : 0.549 9.242 20595 Z= 0.257 Chirality : 0.042 0.133 2290 Planarity : 0.004 0.042 2600 Dihedral : 6.953 64.573 2315 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.41 % Allowed : 10.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1830 helix: 0.32 (0.21), residues: 705 sheet: -0.04 (0.29), residues: 300 loop : 0.10 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 79 HIS 0.004 0.000 HIS B 88 PHE 0.011 0.001 PHE B 223 TYR 0.008 0.001 TYR E 218 ARG 0.003 0.000 ARG C 183 Details of bonding type rmsd hydrogen bonds : bond 0.02828 ( 595) hydrogen bonds : angle 4.11347 ( 1395) covalent geometry : bond 0.00220 (15150) covalent geometry : angle 0.54880 (20595) Misc. bond : bond 0.00033 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 227 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8633 (mtp) REVERT: B 44 MET cc_start: 0.8084 (ttp) cc_final: 0.7473 (tmm) REVERT: B 355 MET cc_start: 0.8720 (mmm) cc_final: 0.8447 (mmm) REVERT: E 47 MET cc_start: 0.6878 (pmm) cc_final: 0.6106 (ttt) REVERT: E 190 MET cc_start: 0.7774 (mmm) cc_final: 0.7491 (mmt) REVERT: E 269 MET cc_start: 0.7157 (mmm) cc_final: 0.6669 (mtt) REVERT: E 355 MET cc_start: 0.7891 (mmm) cc_final: 0.7305 (mtm) REVERT: C 47 MET cc_start: 0.7464 (mtp) cc_final: 0.6959 (mtp) REVERT: C 187 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: A 82 MET cc_start: 0.9038 (tpt) cc_final: 0.8700 (tpp) REVERT: A 124 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8564 (m-80) outliers start: 22 outliers final: 16 residues processed: 116 average time/residue: 0.2194 time to fit residues: 42.3338 Evaluate side-chains 119 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 227 MET 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 370 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 65 LEU 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 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 257 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 84 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 0.0000 chunk 165 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.065069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.052942 restraints weight = 52392.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.055039 restraints weight = 28278.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056503 restraints weight = 18707.821| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15155 Z= 0.187 Angle : 0.621 9.142 20595 Z= 0.295 Chirality : 0.044 0.152 2290 Planarity : 0.004 0.045 2600 Dihedral : 7.150 69.041 2315 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.66 % Allowed : 10.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1830 helix: 0.24 (0.20), residues: 700 sheet: -0.27 (0.28), residues: 345 loop : -0.00 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.002 0.001 HIS E 275 PHE 0.011 0.001 PHE B 223 TYR 0.010 0.001 TYR B 240 ARG 0.002 0.000 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 595) hydrogen bonds : angle 4.37601 ( 1395) covalent geometry : bond 0.00433 (15150) covalent geometry : angle 0.62069 (20595) Misc. bond : bond 0.00030 ( 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 124 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 1.729 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.8121 (ttp) cc_final: 0.7542 (tmm) REVERT: B 187 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8308 (m-30) REVERT: B 227 MET cc_start: 0.8139 (tpp) cc_final: 0.7839 (mpp) REVERT: E 47 MET cc_start: 0.6881 (pmm) cc_final: 0.6195 (ttt) REVERT: E 190 MET cc_start: 0.7790 (mmm) cc_final: 0.7477 (mmt) REVERT: E 269 MET cc_start: 0.7353 (mmm) cc_final: 0.6933 (mtt) REVERT: E 355 MET cc_start: 0.7952 (mmm) cc_final: 0.7296 (mtm) REVERT: C 47 MET cc_start: 0.7484 (mtp) cc_final: 0.6956 (mtp) REVERT: C 269 MET cc_start: 0.8016 (tpp) cc_final: 0.7658 (mmp) REVERT: A 82 MET cc_start: 0.9068 (tpt) cc_final: 0.8499 (tpp) REVERT: A 124 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8600 (m-80) REVERT: A 269 MET cc_start: 0.8272 (mmp) cc_final: 0.7994 (mmp) outliers start: 26 outliers final: 20 residues processed: 117 average time/residue: 0.2225 time to fit residues: 43.0563 Evaluate side-chains 119 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 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 103 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 LYS 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 299 MET Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 145 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 115 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.066363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054214 restraints weight = 52228.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.056359 restraints weight = 28036.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057850 restraints weight = 18452.027| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15155 Z= 0.110 Angle : 0.572 10.159 20595 Z= 0.266 Chirality : 0.042 0.135 2290 Planarity : 0.004 0.044 2600 Dihedral : 6.912 64.654 2315 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.28 % Allowed : 11.25 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1830 helix: 0.39 (0.20), residues: 700 sheet: -0.15 (0.29), residues: 310 loop : 0.00 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 79 HIS 0.003 0.000 HIS B 88 PHE 0.013 0.001 PHE B 223 TYR 0.008 0.001 TYR E 218 ARG 0.003 0.000 ARG E 335 Details of bonding type rmsd hydrogen bonds : bond 0.03016 ( 595) hydrogen bonds : angle 4.14892 ( 1395) covalent geometry : bond 0.00253 (15150) covalent geometry : angle 0.57180 (20595) Misc. bond : bond 0.00032 ( 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 121 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.811 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.8071 (ttp) cc_final: 0.7507 (tmm) REVERT: B 227 MET cc_start: 0.8161 (tpp) cc_final: 0.7869 (mpp) REVERT: E 47 MET cc_start: 0.6755 (pmm) cc_final: 0.6155 (ttt) REVERT: E 190 MET cc_start: 0.7773 (mmm) cc_final: 0.7481 (mmt) REVERT: E 269 MET cc_start: 0.7229 (mmm) cc_final: 0.6792 (mtt) REVERT: E 355 MET cc_start: 0.7873 (mmm) cc_final: 0.7304 (mtm) REVERT: C 47 MET cc_start: 0.7427 (mtp) cc_final: 0.6904 (mtp) REVERT: A 47 MET cc_start: 0.7798 (tmm) cc_final: 0.7475 (tmm) REVERT: A 82 MET cc_start: 0.9053 (tpt) cc_final: 0.8739 (tpp) REVERT: A 124 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8561 (m-80) REVERT: A 269 MET cc_start: 0.8153 (mmp) cc_final: 0.7875 (mmp) outliers start: 20 outliers final: 18 residues processed: 114 average time/residue: 0.2157 time to fit residues: 40.8256 Evaluate side-chains 117 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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 192 ILE 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 352 PHE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 121 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 170 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 177 optimal weight: 0.0570 overall best weight: 0.9858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.067485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.055280 restraints weight = 52326.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.057468 restraints weight = 27969.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.058976 restraints weight = 18348.630| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5019 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= 0.087 Angle : 0.546 10.548 20595 Z= 0.251 Chirality : 0.041 0.131 2290 Planarity : 0.004 0.042 2600 Dihedral : 6.588 59.941 2315 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.28 % Allowed : 11.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.20), residues: 1830 helix: 0.46 (0.21), residues: 705 sheet: -0.06 (0.29), residues: 300 loop : 0.09 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 79 HIS 0.004 0.000 HIS B 88 PHE 0.012 0.001 PHE B 223 TYR 0.009 0.001 TYR E 279 ARG 0.001 0.000 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.02489 ( 595) hydrogen bonds : angle 3.97774 ( 1395) covalent geometry : bond 0.00197 (15150) covalent geometry : angle 0.54636 (20595) Misc. bond : bond 0.00031 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4162.32 seconds wall clock time: 75 minutes 52.04 seconds (4552.04 seconds total)