Starting phenix.real_space_refine on Fri May 16 20:17:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hm9_52289/05_2025/9hm9_52289.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hm9_52289/05_2025/9hm9_52289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hm9_52289/05_2025/9hm9_52289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hm9_52289/05_2025/9hm9_52289.map" model { file = "/net/cci-nas-00/data/ceres_data/9hm9_52289/05_2025/9hm9_52289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hm9_52289/05_2025/9hm9_52289.cif" } resolution = 3.4 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= -0.001 sd= 0.069 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 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9332 2.51 5 N 2503 2.21 5 O 2843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14798 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" 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: "F" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 158 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 19} 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: "E" 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: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.70, per 1000 atoms: 0.66 Number of scatterers: 14798 At special positions: 0 Unit cell: (99.84, 76.96, 191.36, 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 10 15.00 Mg 5 11.99 O 2843 8.00 N 2503 7.00 C 9332 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=0, symmetry=0 Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 1.9 seconds 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 25 sheets defined 52.6% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.707A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.746A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.534A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.537A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 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: 3.676A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.700A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.700A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.777A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 37 removed outlier: 3.947A pdb=" N LEU F 27 " --> pdb=" O GLY F 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.674A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.798A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.902A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.524A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 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: 3.672A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.641A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.547A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.777A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.680A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.774A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.889A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 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: 3.649A pdb=" N ASP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 234 through 237 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 285 Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 349 removed outlier: 3.655A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.541A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.797A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.751A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.767A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.501A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.531A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 194 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: 3.679A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.670A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.551A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.794A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.677A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.771A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.535A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.515A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 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: 3.661A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.630A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.563A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.800A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.844A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.595A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.545A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.658A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.655A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'A' and resid 176 through 177 removed outlier: 6.489A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.903A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'E' and resid 176 through 177 removed outlier: 6.932A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.707A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.692A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'B' and resid 176 through 177 removed outlier: 6.553A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.944A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.616A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'D' and resid 176 through 177 removed outlier: 6.601A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 238 through 241 707 hydrogen bonds defined for protein. 1848 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: 5.46 Time building geometry restraints manager: 4.83 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: 4824 1.34 - 1.46: 3079 1.46 - 1.58: 7016 1.58 - 1.69: 15 1.69 - 1.81: 185 Bond restraints: 15119 Sorted by residual: bond pdb=" CA GLU A 334 " pdb=" CB GLU A 334 " ideal model delta sigma weight residual 1.533 1.551 -0.018 1.66e-02 3.63e+03 1.14e+00 bond pdb=" CA GLU E 334 " pdb=" CB GLU E 334 " ideal model delta sigma weight residual 1.533 1.551 -0.018 1.66e-02 3.63e+03 1.14e+00 bond pdb=" CA GLU B 334 " pdb=" CB GLU B 334 " ideal model delta sigma weight residual 1.533 1.551 -0.018 1.66e-02 3.63e+03 1.12e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.11e+00 bond pdb=" CA GLU D 334 " pdb=" CB GLU D 334 " ideal model delta sigma weight residual 1.533 1.551 -0.017 1.66e-02 3.63e+03 1.10e+00 ... (remaining 15114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 19873 1.76 - 3.53: 550 3.53 - 5.29: 69 5.29 - 7.06: 16 7.06 - 8.82: 10 Bond angle restraints: 20518 Sorted by residual: angle pdb=" N GLY A 182 " pdb=" CA GLY A 182 " pdb=" C GLY A 182 " ideal model delta sigma weight residual 113.27 117.89 -4.62 1.33e+00 5.65e-01 1.21e+01 angle pdb=" CA GLU E 334 " pdb=" CB GLU E 334 " pdb=" CG GLU E 334 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N GLY B 182 " pdb=" CA GLY B 182 " pdb=" C GLY B 182 " ideal model delta sigma weight residual 113.27 117.76 -4.49 1.33e+00 5.65e-01 1.14e+01 angle pdb=" CA GLU D 334 " pdb=" CB GLU D 334 " pdb=" CG GLU D 334 " ideal model delta sigma weight residual 114.10 120.81 -6.71 2.00e+00 2.50e-01 1.13e+01 angle pdb=" N GLY E 182 " pdb=" CA GLY E 182 " pdb=" C GLY E 182 " ideal model delta sigma weight residual 113.27 117.70 -4.43 1.33e+00 5.65e-01 1.11e+01 ... (remaining 20513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.01: 8572 20.01 - 40.02: 434 40.02 - 60.04: 62 60.04 - 80.05: 18 80.05 - 100.06: 10 Dihedral angle restraints: 9096 sinusoidal: 3676 harmonic: 5420 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 40.06 -100.06 1 2.00e+01 2.50e-03 2.82e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 40.05 -100.05 1 2.00e+01 2.50e-03 2.82e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 40.02 -100.01 1 2.00e+01 2.50e-03 2.82e+01 ... (remaining 9093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1573 0.044 - 0.087: 526 0.087 - 0.131: 146 0.131 - 0.174: 30 0.174 - 0.218: 4 Chirality restraints: 2279 Sorted by residual: chirality pdb=" CA GLU E 334 " pdb=" N GLU E 334 " pdb=" C GLU E 334 " pdb=" CB GLU E 334 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA GLU A 334 " pdb=" N GLU A 334 " pdb=" C GLU A 334 " pdb=" CB GLU A 334 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA GLU D 334 " pdb=" N GLU D 334 " pdb=" C GLU D 334 " pdb=" CB GLU D 334 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2276 not shown) Planarity restraints: 2624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 183 " -0.260 9.50e-02 1.11e+02 1.17e-01 1.06e+01 pdb=" NE ARG B 183 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 183 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B 183 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 183 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 183 " -0.255 9.50e-02 1.11e+02 1.15e-01 1.05e+01 pdb=" NE ARG D 183 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG D 183 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG D 183 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG D 183 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 183 " -0.257 9.50e-02 1.11e+02 1.16e-01 1.04e+01 pdb=" NE ARG E 183 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG E 183 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG E 183 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG E 183 " -0.001 2.00e-02 2.50e+03 ... (remaining 2621 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 112 2.58 - 3.16: 12715 3.16 - 3.74: 22796 3.74 - 4.32: 34013 4.32 - 4.90: 55123 Nonbonded interactions: 124759 Sorted by model distance: nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 2.003 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.039 2.170 nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 2.062 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 2.083 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.092 2.170 ... (remaining 124754 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.330 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 37.160 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 : 0.003 0.028 15119 Z= 0.133 Angle : 0.727 8.823 20518 Z= 0.406 Chirality : 0.048 0.218 2279 Planarity : 0.011 0.117 2624 Dihedral : 13.192 100.061 5626 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -1.83 (0.18), residues: 1849 helix: -1.85 (0.14), residues: 806 sheet: -1.00 (0.30), residues: 295 loop : -0.22 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP E 86 HIS 0.002 0.001 HIS E 87 PHE 0.008 0.001 PHE E 200 TYR 0.021 0.004 TYR D 188 ARG 0.027 0.005 ARG D 183 Details of bonding type rmsd hydrogen bonds : bond 0.14714 ( 707) hydrogen bonds : angle 7.47493 ( 1848) covalent geometry : bond 0.00278 (15119) covalent geometry : angle 0.72728 (20518) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3240 time to fit residues: 49.5323 Evaluate side-chains 86 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 78 optimal weight: 0.0870 chunk 48 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 169 optimal weight: 9.9990 overall best weight: 3.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN C 173 HIS ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN E 115 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS D 115 ASN D 173 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.023280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.019135 restraints weight = 155153.773| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 4.74 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15119 Z= 0.172 Angle : 0.642 9.095 20518 Z= 0.319 Chirality : 0.044 0.169 2279 Planarity : 0.004 0.043 2624 Dihedral : 6.891 70.623 2110 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.13 % Allowed : 2.66 % Favored : 97.21 % 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: 0.32 (0.20), residues: 1849 helix: 0.32 (0.18), residues: 791 sheet: -0.51 (0.30), residues: 295 loop : 0.70 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.002 0.001 HIS D 101 PHE 0.018 0.001 PHE D 375 TYR 0.013 0.001 TYR C 294 ARG 0.005 0.001 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 707) hydrogen bonds : angle 5.63128 ( 1848) covalent geometry : bond 0.00375 (15119) covalent geometry : angle 0.64167 (20518) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 227 MET cc_start: 0.9281 (tpp) cc_final: 0.8934 (mmm) REVERT: A 82 MET cc_start: 0.9420 (tpt) cc_final: 0.9119 (tpt) REVERT: A 132 MET cc_start: 0.8881 (tmm) cc_final: 0.8655 (tmm) REVERT: A 176 MET cc_start: 0.8210 (mtp) cc_final: 0.7987 (mtm) REVERT: A 227 MET cc_start: 0.9235 (mmm) cc_final: 0.8806 (tpp) REVERT: A 375 PHE cc_start: 0.8000 (m-80) cc_final: 0.7762 (m-10) REVERT: E 82 MET cc_start: 0.9139 (tpp) cc_final: 0.8753 (tpp) REVERT: B 82 MET cc_start: 0.9421 (tpt) cc_final: 0.8821 (tpt) REVERT: B 227 MET cc_start: 0.9182 (mmm) cc_final: 0.8959 (mmm) REVERT: B 269 MET cc_start: 0.9288 (tpp) cc_final: 0.9020 (mtt) REVERT: B 325 MET cc_start: 0.9271 (mmp) cc_final: 0.8948 (mmt) REVERT: B 355 MET cc_start: 0.9270 (mmm) cc_final: 0.9036 (mpp) REVERT: D 44 MET cc_start: 0.8862 (tpp) cc_final: 0.8421 (tpp) REVERT: D 82 MET cc_start: 0.8932 (tpp) cc_final: 0.8569 (tpp) REVERT: D 176 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8310 (mpp) REVERT: D 227 MET cc_start: 0.9162 (mmm) cc_final: 0.8914 (mmm) outliers start: 2 outliers final: 0 residues processed: 91 average time/residue: 0.2473 time to fit residues: 35.8772 Evaluate side-chains 86 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 128 optimal weight: 20.0000 chunk 104 optimal weight: 0.0980 chunk 140 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS A 297 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.023269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.019137 restraints weight = 155860.952| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 4.72 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15119 Z= 0.127 Angle : 0.581 8.608 20518 Z= 0.284 Chirality : 0.043 0.144 2279 Planarity : 0.004 0.046 2624 Dihedral : 5.826 50.372 2110 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.06 % Allowed : 3.29 % Favored : 96.64 % 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: 0.74 (0.20), residues: 1849 helix: 0.88 (0.18), residues: 821 sheet: -0.27 (0.31), residues: 295 loop : 0.62 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 79 HIS 0.002 0.001 HIS A 101 PHE 0.011 0.001 PHE D 375 TYR 0.009 0.001 TYR A 188 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 707) hydrogen bonds : angle 5.14793 ( 1848) covalent geometry : bond 0.00277 (15119) covalent geometry : angle 0.58100 (20518) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 44 MET cc_start: 0.8780 (tpp) cc_final: 0.8486 (tpp) REVERT: C 132 MET cc_start: 0.8587 (tmm) cc_final: 0.8352 (tmm) REVERT: C 227 MET cc_start: 0.9239 (tpp) cc_final: 0.8797 (tpp) REVERT: C 269 MET cc_start: 0.9030 (tpp) cc_final: 0.8652 (mtt) REVERT: A 44 MET cc_start: -0.2277 (pmm) cc_final: -0.2636 (pmm) REVERT: A 82 MET cc_start: 0.9521 (tpt) cc_final: 0.9187 (tpt) REVERT: A 176 MET cc_start: 0.8284 (mtp) cc_final: 0.8080 (mtm) REVERT: A 227 MET cc_start: 0.9232 (mmm) cc_final: 0.9021 (mmm) REVERT: A 305 MET cc_start: 0.8800 (mmm) cc_final: 0.8502 (mmm) REVERT: A 375 PHE cc_start: 0.7887 (m-80) cc_final: 0.7614 (m-10) REVERT: E 47 MET cc_start: 0.2359 (ptm) cc_final: 0.1538 (mtt) REVERT: E 82 MET cc_start: 0.9203 (tpp) cc_final: 0.8673 (tpp) REVERT: E 269 MET cc_start: 0.9246 (tpp) cc_final: 0.8720 (mtt) REVERT: B 82 MET cc_start: 0.9466 (tpt) cc_final: 0.8748 (tpt) REVERT: B 227 MET cc_start: 0.9188 (mmm) cc_final: 0.8904 (mmm) REVERT: B 269 MET cc_start: 0.9274 (tpp) cc_final: 0.9035 (mtt) REVERT: B 283 MET cc_start: 0.9345 (mmm) cc_final: 0.9065 (mmm) REVERT: B 325 MET cc_start: 0.9247 (mmp) cc_final: 0.8999 (mmt) REVERT: D 44 MET cc_start: 0.9027 (tpp) cc_final: 0.8228 (tpp) REVERT: D 82 MET cc_start: 0.9040 (tpp) cc_final: 0.8548 (tpp) REVERT: D 176 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8218 (mpp) REVERT: D 227 MET cc_start: 0.9133 (mmm) cc_final: 0.8883 (mmm) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.2409 time to fit residues: 33.9026 Evaluate side-chains 87 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 74 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.022795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.018637 restraints weight = 161537.691| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 4.70 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15119 Z= 0.261 Angle : 0.654 9.351 20518 Z= 0.320 Chirality : 0.044 0.144 2279 Planarity : 0.004 0.044 2624 Dihedral : 5.845 50.021 2110 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.32 % Allowed : 3.80 % Favored : 95.88 % 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: 0.97 (0.21), residues: 1849 helix: 1.15 (0.18), residues: 816 sheet: -0.52 (0.30), residues: 315 loop : 0.87 (0.26), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 79 HIS 0.004 0.001 HIS C 371 PHE 0.013 0.001 PHE D 262 TYR 0.008 0.001 TYR A 53 ARG 0.003 0.001 ARG C 183 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 707) hydrogen bonds : angle 5.10901 ( 1848) covalent geometry : bond 0.00558 (15119) covalent geometry : angle 0.65420 (20518) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 1.698 Fit side-chains revert: symmetry clash REVERT: C 82 MET cc_start: 0.9379 (tpt) cc_final: 0.9095 (tpt) REVERT: C 132 MET cc_start: 0.8618 (tmm) cc_final: 0.8313 (tmm) REVERT: C 227 MET cc_start: 0.9298 (tpp) cc_final: 0.8883 (mmm) REVERT: C 269 MET cc_start: 0.9106 (tpp) cc_final: 0.8725 (mtt) REVERT: C 299 MET cc_start: 0.9198 (mmm) cc_final: 0.8689 (mmp) REVERT: A 44 MET cc_start: -0.2756 (pmm) cc_final: -0.3154 (ptp) REVERT: A 82 MET cc_start: 0.9515 (tpt) cc_final: 0.9301 (tpt) REVERT: A 176 MET cc_start: 0.8350 (mtp) cc_final: 0.8087 (mtm) REVERT: A 227 MET cc_start: 0.9297 (mmm) cc_final: 0.9066 (mmm) REVERT: A 299 MET cc_start: 0.9139 (mtp) cc_final: 0.8717 (ptp) REVERT: A 305 MET cc_start: 0.8922 (mmm) cc_final: 0.8666 (mmm) REVERT: A 355 MET cc_start: 0.9413 (mmp) cc_final: 0.9123 (mmp) REVERT: A 375 PHE cc_start: 0.8078 (m-80) cc_final: 0.7831 (m-10) REVERT: E 47 MET cc_start: 0.2547 (ptm) cc_final: 0.1102 (mtt) REVERT: E 82 MET cc_start: 0.9155 (tpp) cc_final: 0.8815 (tpp) REVERT: E 132 MET cc_start: 0.8827 (tmm) cc_final: 0.8282 (tmm) REVERT: E 269 MET cc_start: 0.9247 (tpp) cc_final: 0.8674 (mtt) REVERT: B 82 MET cc_start: 0.9460 (tpt) cc_final: 0.9044 (tpt) REVERT: B 176 MET cc_start: 0.9023 (mtt) cc_final: 0.8789 (mtt) REVERT: B 227 MET cc_start: 0.9305 (mmm) cc_final: 0.9075 (mmm) REVERT: B 269 MET cc_start: 0.9292 (tpp) cc_final: 0.9080 (mtt) REVERT: B 325 MET cc_start: 0.9217 (mmp) cc_final: 0.8988 (mmm) REVERT: D 44 MET cc_start: 0.8834 (tpp) cc_final: 0.8324 (tpp) REVERT: D 47 MET cc_start: 0.8281 (pmm) cc_final: 0.8068 (pmm) REVERT: D 123 MET cc_start: 0.9199 (mmm) cc_final: 0.8977 (mmm) REVERT: D 176 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8211 (mpp) REVERT: D 227 MET cc_start: 0.9186 (mmm) cc_final: 0.8974 (mmm) outliers start: 5 outliers final: 0 residues processed: 91 average time/residue: 0.2373 time to fit residues: 34.3598 Evaluate side-chains 87 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 148 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.023549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.019315 restraints weight = 156970.153| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 4.79 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15119 Z= 0.118 Angle : 0.572 9.933 20518 Z= 0.275 Chirality : 0.042 0.136 2279 Planarity : 0.004 0.047 2624 Dihedral : 5.470 44.670 2110 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.32 % Allowed : 4.37 % Favored : 95.31 % 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: 1.21 (0.21), residues: 1849 helix: 1.42 (0.19), residues: 818 sheet: -0.20 (0.31), residues: 295 loop : 0.75 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.002 0.001 HIS A 101 PHE 0.010 0.001 PHE C 375 TYR 0.008 0.001 TYR E 188 ARG 0.002 0.000 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.02925 ( 707) hydrogen bonds : angle 4.75567 ( 1848) covalent geometry : bond 0.00260 (15119) covalent geometry : angle 0.57191 (20518) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.762 Fit side-chains revert: symmetry clash REVERT: C 82 MET cc_start: 0.9348 (tpt) cc_final: 0.8874 (tpt) REVERT: C 227 MET cc_start: 0.9247 (tpp) cc_final: 0.8780 (tpp) REVERT: C 269 MET cc_start: 0.9065 (tpp) cc_final: 0.8705 (mtt) REVERT: C 299 MET cc_start: 0.9082 (mmm) cc_final: 0.8458 (mmp) REVERT: A 44 MET cc_start: -0.2717 (pmm) cc_final: -0.3155 (ptp) REVERT: A 82 MET cc_start: 0.9501 (tpt) cc_final: 0.9250 (tpt) REVERT: A 176 MET cc_start: 0.8334 (mtp) cc_final: 0.7971 (mtm) REVERT: A 227 MET cc_start: 0.9240 (mmm) cc_final: 0.8998 (mmm) REVERT: A 269 MET cc_start: 0.9135 (tpp) cc_final: 0.8764 (tpp) REVERT: A 299 MET cc_start: 0.9104 (mtp) cc_final: 0.8663 (ptp) REVERT: A 305 MET cc_start: 0.9005 (mmm) cc_final: 0.8718 (mmm) REVERT: A 355 MET cc_start: 0.9445 (mmp) cc_final: 0.9207 (mmp) REVERT: A 375 PHE cc_start: 0.7875 (m-80) cc_final: 0.7568 (m-10) REVERT: E 43 VAL cc_start: 0.9324 (m) cc_final: 0.9064 (m) REVERT: E 47 MET cc_start: 0.2161 (ptm) cc_final: 0.0764 (mtt) REVERT: E 132 MET cc_start: 0.8858 (tmm) cc_final: 0.8338 (tmm) REVERT: E 269 MET cc_start: 0.9201 (tpp) cc_final: 0.8735 (mtt) REVERT: B 82 MET cc_start: 0.9420 (tpt) cc_final: 0.9165 (tpt) REVERT: B 176 MET cc_start: 0.9007 (mtt) cc_final: 0.8788 (mtt) REVERT: B 227 MET cc_start: 0.9216 (mmm) cc_final: 0.8961 (mmm) REVERT: B 325 MET cc_start: 0.9169 (mmp) cc_final: 0.8943 (mmm) REVERT: D 44 MET cc_start: 0.8822 (tpp) cc_final: 0.8371 (tpp) REVERT: D 123 MET cc_start: 0.9149 (mmm) cc_final: 0.8881 (mmm) REVERT: D 132 MET cc_start: 0.8676 (tmm) cc_final: 0.8428 (tmm) REVERT: D 176 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8149 (mpp) REVERT: D 227 MET cc_start: 0.9169 (mmm) cc_final: 0.8961 (mmm) REVERT: D 283 MET cc_start: 0.9212 (mmm) cc_final: 0.8980 (mmm) REVERT: D 299 MET cc_start: 0.8943 (mtp) cc_final: 0.8690 (mmt) outliers start: 5 outliers final: 3 residues processed: 93 average time/residue: 0.2422 time to fit residues: 35.9325 Evaluate side-chains 92 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 176 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 48 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 150 optimal weight: 20.0000 chunk 167 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 184 optimal weight: 4.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 115 ASN D 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.022330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.018198 restraints weight = 160357.230| |-----------------------------------------------------------------------------| r_work (start): 0.2530 rms_B_bonded: 4.66 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 15119 Z= 0.321 Angle : 0.703 10.690 20518 Z= 0.342 Chirality : 0.044 0.149 2279 Planarity : 0.005 0.044 2624 Dihedral : 5.921 59.876 2110 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.19 % Allowed : 5.89 % Favored : 93.92 % 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: 1.10 (0.21), residues: 1849 helix: 1.33 (0.18), residues: 813 sheet: -0.52 (0.30), residues: 315 loop : 0.87 (0.26), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 79 HIS 0.006 0.001 HIS C 371 PHE 0.014 0.002 PHE D 262 TYR 0.009 0.001 TYR A 169 ARG 0.003 0.001 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 707) hydrogen bonds : angle 5.08431 ( 1848) covalent geometry : bond 0.00683 (15119) covalent geometry : angle 0.70311 (20518) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 1.819 Fit side-chains REVERT: C 82 MET cc_start: 0.9390 (tpt) cc_final: 0.8883 (tpt) REVERT: C 119 MET cc_start: 0.9373 (mtp) cc_final: 0.9001 (mtt) REVERT: C 227 MET cc_start: 0.9336 (tpp) cc_final: 0.8924 (mmm) REVERT: C 269 MET cc_start: 0.9059 (tpp) cc_final: 0.8708 (mtt) REVERT: A 82 MET cc_start: 0.9485 (tpt) cc_final: 0.9069 (tpt) REVERT: A 227 MET cc_start: 0.9316 (mmm) cc_final: 0.9092 (mmm) REVERT: A 299 MET cc_start: 0.9162 (mtp) cc_final: 0.8659 (ptp) REVERT: A 305 MET cc_start: 0.9001 (mmm) cc_final: 0.8747 (mmm) REVERT: A 375 PHE cc_start: 0.8210 (m-80) cc_final: 0.7975 (m-10) REVERT: B 82 MET cc_start: 0.9392 (tpt) cc_final: 0.8828 (tpt) REVERT: B 227 MET cc_start: 0.9347 (mmm) cc_final: 0.8986 (mmm) REVERT: B 325 MET cc_start: 0.9164 (mmp) cc_final: 0.8900 (mmm) REVERT: D 44 MET cc_start: 0.8990 (tpp) cc_final: 0.8711 (tpp) REVERT: D 47 MET cc_start: 0.8322 (pmm) cc_final: 0.8074 (pmm) REVERT: D 132 MET cc_start: 0.8700 (tmm) cc_final: 0.8391 (tmm) REVERT: D 176 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8181 (mpp) REVERT: D 283 MET cc_start: 0.9193 (mmm) cc_final: 0.8993 (mmm) REVERT: D 299 MET cc_start: 0.8944 (mtp) cc_final: 0.8713 (mmt) outliers start: 3 outliers final: 1 residues processed: 88 average time/residue: 0.2508 time to fit residues: 35.1227 Evaluate side-chains 88 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain D residue 176 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 92 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.022552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.018437 restraints weight = 158991.578| |-----------------------------------------------------------------------------| r_work (start): 0.2549 rms_B_bonded: 4.71 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15119 Z= 0.207 Angle : 0.642 11.434 20518 Z= 0.305 Chirality : 0.043 0.133 2279 Planarity : 0.004 0.044 2624 Dihedral : 5.752 57.762 2110 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.38 % Allowed : 6.40 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.18 (0.21), residues: 1849 helix: 1.46 (0.19), residues: 813 sheet: -0.35 (0.30), residues: 305 loop : 0.73 (0.26), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 79 HIS 0.004 0.001 HIS C 371 PHE 0.010 0.001 PHE D 262 TYR 0.010 0.001 TYR C 169 ARG 0.004 0.000 ARG F 32 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 707) hydrogen bonds : angle 4.87307 ( 1848) covalent geometry : bond 0.00448 (15119) covalent geometry : angle 0.64154 (20518) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 1.635 Fit side-chains REVERT: C 82 MET cc_start: 0.9367 (tpt) cc_final: 0.8808 (tpt) REVERT: C 119 MET cc_start: 0.9335 (mtp) cc_final: 0.8969 (mtt) REVERT: C 227 MET cc_start: 0.9302 (tpp) cc_final: 0.8956 (mmm) REVERT: C 269 MET cc_start: 0.9039 (tpp) cc_final: 0.8692 (mtt) REVERT: A 82 MET cc_start: 0.9484 (tpt) cc_final: 0.9069 (tpt) REVERT: A 227 MET cc_start: 0.9277 (mmm) cc_final: 0.9052 (mmm) REVERT: A 269 MET cc_start: 0.9108 (tpp) cc_final: 0.8763 (tpp) REVERT: A 299 MET cc_start: 0.9052 (mtp) cc_final: 0.8706 (ptp) REVERT: A 305 MET cc_start: 0.9040 (mmm) cc_final: 0.8771 (mmm) REVERT: A 375 PHE cc_start: 0.8055 (m-80) cc_final: 0.7814 (m-10) REVERT: E 47 MET cc_start: 0.3693 (ptp) cc_final: 0.1146 (tpp) REVERT: E 269 MET cc_start: 0.9250 (tpp) cc_final: 0.8780 (mtt) REVERT: B 82 MET cc_start: 0.9366 (tpt) cc_final: 0.9052 (tpt) REVERT: B 176 MET cc_start: 0.9073 (mtt) cc_final: 0.8863 (mtt) REVERT: B 227 MET cc_start: 0.9310 (mmm) cc_final: 0.9069 (mmm) REVERT: D 44 MET cc_start: 0.8944 (tpp) cc_final: 0.8674 (tpp) REVERT: D 47 MET cc_start: 0.8293 (pmm) cc_final: 0.8043 (pmm) REVERT: D 132 MET cc_start: 0.8715 (tmm) cc_final: 0.8413 (tmm) REVERT: D 176 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8200 (mpp) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 0.2275 time to fit residues: 33.4149 Evaluate side-chains 91 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain D residue 176 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 112 optimal weight: 0.0170 chunk 75 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 152 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.023665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.019468 restraints weight = 155583.056| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 4.78 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15119 Z= 0.095 Angle : 0.604 12.185 20518 Z= 0.280 Chirality : 0.042 0.140 2279 Planarity : 0.004 0.045 2624 Dihedral : 5.325 57.174 2110 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.32 % Allowed : 6.78 % Favored : 92.91 % 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: 1.34 (0.21), residues: 1849 helix: 1.62 (0.19), residues: 818 sheet: -0.16 (0.31), residues: 295 loop : 0.70 (0.26), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 356 HIS 0.003 0.001 HIS D 275 PHE 0.006 0.001 PHE D 375 TYR 0.009 0.001 TYR D 188 ARG 0.004 0.000 ARG F 32 Details of bonding type rmsd hydrogen bonds : bond 0.02781 ( 707) hydrogen bonds : angle 4.56954 ( 1848) covalent geometry : bond 0.00212 (15119) covalent geometry : angle 0.60423 (20518) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.775 Fit side-chains revert: symmetry clash REVERT: C 82 MET cc_start: 0.9383 (tpt) cc_final: 0.9042 (tpt) REVERT: C 227 MET cc_start: 0.9218 (tpp) cc_final: 0.8836 (mmm) REVERT: C 269 MET cc_start: 0.9126 (tpp) cc_final: 0.8687 (mtt) REVERT: C 305 MET cc_start: 0.9230 (mmm) cc_final: 0.8853 (mmm) REVERT: A 82 MET cc_start: 0.9474 (tpt) cc_final: 0.9078 (tpt) REVERT: A 227 MET cc_start: 0.9282 (mmm) cc_final: 0.9063 (mmm) REVERT: A 269 MET cc_start: 0.9130 (tpp) cc_final: 0.8797 (tpp) REVERT: A 299 MET cc_start: 0.9087 (mtp) cc_final: 0.8774 (ptp) REVERT: A 305 MET cc_start: 0.9097 (mmm) cc_final: 0.8838 (mmm) REVERT: E 132 MET cc_start: 0.8903 (tmm) cc_final: 0.8628 (tmm) REVERT: E 269 MET cc_start: 0.9204 (tpp) cc_final: 0.8836 (mtt) REVERT: B 82 MET cc_start: 0.9373 (tpt) cc_final: 0.9028 (tpt) REVERT: B 132 MET cc_start: 0.9058 (tmm) cc_final: 0.8853 (tmm) REVERT: B 227 MET cc_start: 0.9206 (mmm) cc_final: 0.8949 (mmm) REVERT: D 44 MET cc_start: 0.8897 (tpp) cc_final: 0.8581 (tpp) REVERT: D 119 MET cc_start: 0.8991 (mtp) cc_final: 0.8649 (mtt) REVERT: D 176 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8135 (mpp) outliers start: 5 outliers final: 4 residues processed: 92 average time/residue: 0.2213 time to fit residues: 33.3326 Evaluate side-chains 91 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 176 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 136 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.023086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.018932 restraints weight = 155504.404| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 4.76 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15119 Z= 0.154 Angle : 0.619 12.642 20518 Z= 0.289 Chirality : 0.042 0.135 2279 Planarity : 0.004 0.046 2624 Dihedral : 5.364 58.727 2110 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.44 % Allowed : 7.03 % Favored : 92.53 % 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: 1.29 (0.21), residues: 1849 helix: 1.43 (0.18), residues: 848 sheet: -0.24 (0.31), residues: 305 loop : 0.89 (0.27), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.003 0.001 HIS B 275 PHE 0.010 0.001 PHE C 375 TYR 0.007 0.001 TYR A 169 ARG 0.003 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.02885 ( 707) hydrogen bonds : angle 4.66911 ( 1848) covalent geometry : bond 0.00338 (15119) covalent geometry : angle 0.61933 (20518) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 1.697 Fit side-chains REVERT: C 82 MET cc_start: 0.9405 (tpt) cc_final: 0.8795 (tpt) REVERT: C 227 MET cc_start: 0.9283 (tpp) cc_final: 0.8956 (mmm) REVERT: C 269 MET cc_start: 0.9079 (tpp) cc_final: 0.8689 (mtt) REVERT: C 305 MET cc_start: 0.9242 (mmm) cc_final: 0.8762 (mmm) REVERT: A 82 MET cc_start: 0.9523 (tpt) cc_final: 0.9139 (tpt) REVERT: A 227 MET cc_start: 0.9292 (mmm) cc_final: 0.9067 (mmm) REVERT: A 269 MET cc_start: 0.9163 (tpp) cc_final: 0.8821 (tpp) REVERT: A 305 MET cc_start: 0.9095 (mmm) cc_final: 0.8842 (mmm) REVERT: E 132 MET cc_start: 0.8934 (tmm) cc_final: 0.8298 (tmm) REVERT: E 269 MET cc_start: 0.9239 (tpp) cc_final: 0.8810 (mtt) REVERT: B 82 MET cc_start: 0.9379 (tpt) cc_final: 0.9010 (tpt) REVERT: B 227 MET cc_start: 0.9256 (mmm) cc_final: 0.8990 (mmm) REVERT: D 44 MET cc_start: 0.8897 (tpp) cc_final: 0.8636 (tpp) REVERT: D 176 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8201 (mpp) REVERT: D 283 MET cc_start: 0.9256 (mmm) cc_final: 0.9008 (mmm) outliers start: 7 outliers final: 4 residues processed: 88 average time/residue: 0.2341 time to fit residues: 33.6383 Evaluate side-chains 90 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain D residue 176 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 17 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 152 optimal weight: 0.1980 chunk 114 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.022989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.018859 restraints weight = 156998.818| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 4.75 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15119 Z= 0.163 Angle : 0.648 13.309 20518 Z= 0.298 Chirality : 0.042 0.138 2279 Planarity : 0.004 0.046 2624 Dihedral : 5.397 59.997 2110 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.32 % Allowed : 7.16 % Favored : 92.53 % 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: 1.26 (0.21), residues: 1849 helix: 1.41 (0.18), residues: 848 sheet: -0.27 (0.31), residues: 305 loop : 0.89 (0.27), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 79 HIS 0.003 0.001 HIS B 275 PHE 0.008 0.001 PHE F 29 TYR 0.010 0.001 TYR B 294 ARG 0.004 0.000 ARG F 32 Details of bonding type rmsd hydrogen bonds : bond 0.02907 ( 707) hydrogen bonds : angle 4.69257 ( 1848) covalent geometry : bond 0.00357 (15119) covalent geometry : angle 0.64752 (20518) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3698 Ramachandran restraints generated. 1849 Oldfield, 0 Emsley, 1849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.613 Fit side-chains revert: symmetry clash REVERT: C 82 MET cc_start: 0.9397 (tpt) cc_final: 0.9033 (tpt) REVERT: C 227 MET cc_start: 0.9277 (tpp) cc_final: 0.8974 (mmm) REVERT: C 269 MET cc_start: 0.9111 (tpp) cc_final: 0.8683 (mtt) REVERT: C 305 MET cc_start: 0.9239 (mmm) cc_final: 0.8776 (mmm) REVERT: A 82 MET cc_start: 0.9525 (tpt) cc_final: 0.9128 (tpt) REVERT: A 227 MET cc_start: 0.9295 (mmm) cc_final: 0.9070 (mmm) REVERT: A 269 MET cc_start: 0.9172 (tpp) cc_final: 0.8817 (tpp) REVERT: A 305 MET cc_start: 0.9090 (mmm) cc_final: 0.8845 (mmm) REVERT: E 269 MET cc_start: 0.9228 (tpp) cc_final: 0.8799 (mtt) REVERT: B 82 MET cc_start: 0.9420 (tpt) cc_final: 0.9203 (tpt) REVERT: B 227 MET cc_start: 0.9253 (mmm) cc_final: 0.8986 (mmm) REVERT: D 44 MET cc_start: 0.8910 (tpp) cc_final: 0.8656 (tpp) REVERT: D 47 MET cc_start: 0.8277 (pmm) cc_final: 0.8021 (pmm) REVERT: D 119 MET cc_start: 0.9219 (mtp) cc_final: 0.8940 (mtt) REVERT: D 176 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8191 (mpp) REVERT: D 227 MET cc_start: 0.9279 (mmm) cc_final: 0.8970 (mmm) REVERT: D 283 MET cc_start: 0.9262 (mmm) cc_final: 0.9034 (mmm) outliers start: 5 outliers final: 4 residues processed: 87 average time/residue: 0.2245 time to fit residues: 31.8387 Evaluate side-chains 90 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain D residue 176 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 77 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.022700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.018586 restraints weight = 159160.305| |-----------------------------------------------------------------------------| r_work (start): 0.2545 rms_B_bonded: 4.71 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15119 Z= 0.239 Angle : 0.689 13.151 20518 Z= 0.323 Chirality : 0.043 0.137 2279 Planarity : 0.004 0.045 2624 Dihedral : 5.628 54.968 2110 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.38 % Allowed : 7.09 % Favored : 92.53 % 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: 1.14 (0.21), residues: 1849 helix: 1.32 (0.18), residues: 848 sheet: -0.41 (0.31), residues: 310 loop : 0.86 (0.27), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 79 HIS 0.005 0.001 HIS C 371 PHE 0.011 0.001 PHE D 262 TYR 0.009 0.001 TYR A 169 ARG 0.004 0.000 ARG F 32 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 707) hydrogen bonds : angle 4.85324 ( 1848) covalent geometry : bond 0.00513 (15119) covalent geometry : angle 0.68905 (20518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4338.84 seconds wall clock time: 77 minutes 22.05 seconds (4642.05 seconds total)