Starting phenix.real_space_refine on Thu Sep 18 06:54:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hm9_52289/09_2025/9hm9_52289.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hm9_52289/09_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_52289/09_2025/9hm9_52289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hm9_52289/09_2025/9hm9_52289.map" model { file = "/net/cci-nas-00/data/ceres_data/9hm9_52289/09_2025/9hm9_52289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hm9_52289/09_2025/9hm9_52289.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.069 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.94, per 1000 atoms: 0.27 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: 1.36 Conformation dependent library (CDL) restraints added in 670.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.67 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: 2.70 Time building geometry restraints manager: 1.79 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: 1.790 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.510 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.260 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.027 0.005 ARG D 183 TYR 0.021 0.004 TYR D 188 PHE 0.008 0.001 PHE E 200 TRP 0.027 0.004 TRP E 86 HIS 0.002 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00278 (15119) covalent geometry : angle 0.72728 (20518) hydrogen bonds : bond 0.14714 ( 707) hydrogen bonds : angle 7.47493 ( 1848) *********************** 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 : 0.512 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: 0.1393 time to fit residues: 21.2588 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 : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.0570 overall best weight: 4.6104 ------------------------------------------------------------------------------- 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 B 173 HIS D 111 ASN D 115 ASN D 173 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.022953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.018841 restraints weight = 157147.630| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 4.69 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1971 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= 0.213 Angle : 0.667 9.055 20518 Z= 0.331 Chirality : 0.044 0.171 2279 Planarity : 0.004 0.042 2624 Dihedral : 6.873 70.125 2110 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.13 % Allowed : 2.79 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.20), residues: 1849 helix: 0.40 (0.18), residues: 786 sheet: -0.63 (0.29), residues: 305 loop : 0.70 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 177 TYR 0.014 0.001 TYR C 294 PHE 0.017 0.002 PHE D 375 TRP 0.016 0.002 TRP D 79 HIS 0.002 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00463 (15119) covalent geometry : angle 0.66712 (20518) hydrogen bonds : bond 0.03726 ( 707) hydrogen bonds : angle 5.63852 ( 1848) *********************** 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 : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 227 MET cc_start: 0.9278 (tpp) cc_final: 0.8936 (mmm) REVERT: A 82 MET cc_start: 0.9473 (tpt) cc_final: 0.9166 (tpt) REVERT: A 132 MET cc_start: 0.8935 (tmm) cc_final: 0.8708 (tmm) REVERT: A 176 MET cc_start: 0.8286 (mtp) cc_final: 0.7953 (mtm) REVERT: A 227 MET cc_start: 0.9273 (mmm) cc_final: 0.8852 (tpp) REVERT: A 355 MET cc_start: 0.9325 (mmm) cc_final: 0.8693 (mpp) REVERT: A 375 PHE cc_start: 0.8077 (m-80) cc_final: 0.7848 (m-10) REVERT: E 82 MET cc_start: 0.9098 (tpp) cc_final: 0.8692 (tpp) REVERT: B 82 MET cc_start: 0.9459 (tpt) cc_final: 0.8798 (tpt) REVERT: B 176 MET cc_start: 0.8939 (mtt) cc_final: 0.8719 (mtt) REVERT: B 227 MET cc_start: 0.9209 (mmm) cc_final: 0.8971 (mmm) REVERT: B 269 MET cc_start: 0.9260 (tpp) cc_final: 0.9049 (mtt) REVERT: B 313 MET cc_start: 0.9535 (tpp) cc_final: 0.9308 (tpp) REVERT: B 325 MET cc_start: 0.9223 (mmp) cc_final: 0.8948 (mmp) REVERT: B 355 MET cc_start: 0.9283 (mmm) cc_final: 0.9063 (mpp) REVERT: D 44 MET cc_start: 0.8799 (tpp) cc_final: 0.7909 (tpp) REVERT: D 82 MET cc_start: 0.8933 (tpp) cc_final: 0.8528 (tpp) REVERT: D 176 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8282 (mpp) REVERT: D 227 MET cc_start: 0.9175 (mmm) cc_final: 0.8942 (mmm) outliers start: 2 outliers final: 0 residues processed: 91 average time/residue: 0.1049 time to fit residues: 15.1969 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 : 0.505 ------------------------------------------------------------------------------- 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 91 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 134 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: C 49 GLN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS E 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.022495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.018400 restraints weight = 159991.071| |-----------------------------------------------------------------------------| r_work (start): 0.2559 rms_B_bonded: 4.72 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15119 Z= 0.240 Angle : 0.642 8.197 20518 Z= 0.317 Chirality : 0.044 0.150 2279 Planarity : 0.004 0.044 2624 Dihedral : 6.133 57.506 2110 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.13 % Allowed : 3.67 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.20), residues: 1849 helix: 0.89 (0.18), residues: 816 sheet: -0.43 (0.31), residues: 305 loop : 0.75 (0.26), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 177 TYR 0.009 0.001 TYR D 188 PHE 0.012 0.001 PHE D 262 TRP 0.017 0.002 TRP D 79 HIS 0.004 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00512 (15119) covalent geometry : angle 0.64200 (20518) hydrogen bonds : bond 0.03467 ( 707) hydrogen bonds : angle 5.30350 ( 1848) *********************** 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 91 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 MET cc_start: 0.8826 (tpp) cc_final: 0.8622 (tpt) REVERT: C 227 MET cc_start: 0.9266 (tpp) cc_final: 0.8826 (tpp) REVERT: C 269 MET cc_start: 0.9094 (tpp) cc_final: 0.8677 (mtt) REVERT: A 44 MET cc_start: -0.2599 (pmm) cc_final: -0.3256 (ptp) REVERT: A 82 MET cc_start: 0.9503 (tpt) cc_final: 0.9139 (tpt) REVERT: A 176 MET cc_start: 0.8324 (mtp) cc_final: 0.8072 (mtm) REVERT: A 227 MET cc_start: 0.9278 (mmm) cc_final: 0.8812 (tpp) REVERT: A 305 MET cc_start: 0.8776 (mmm) cc_final: 0.8490 (mmm) REVERT: A 355 MET cc_start: 0.9411 (mmm) cc_final: 0.8730 (mpp) REVERT: A 375 PHE cc_start: 0.8119 (m-80) cc_final: 0.7901 (m-10) REVERT: E 47 MET cc_start: 0.2736 (ptm) cc_final: 0.1796 (mtt) REVERT: E 269 MET cc_start: 0.9307 (tpp) cc_final: 0.8666 (mtt) REVERT: B 82 MET cc_start: 0.9433 (tpt) cc_final: 0.8687 (tpt) REVERT: B 227 MET cc_start: 0.9285 (mmm) cc_final: 0.9024 (mmm) REVERT: B 269 MET cc_start: 0.9297 (tpp) cc_final: 0.9070 (mtt) REVERT: D 44 MET cc_start: 0.9127 (tpp) cc_final: 0.8418 (tpp) REVERT: D 82 MET cc_start: 0.8999 (tpp) cc_final: 0.8588 (tpp) REVERT: D 176 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8536 (mpp) REVERT: D 227 MET cc_start: 0.9160 (mmm) cc_final: 0.8951 (mmm) outliers start: 2 outliers final: 0 residues processed: 90 average time/residue: 0.1139 time to fit residues: 16.4259 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 : 0.569 ------------------------------------------------------------------------------- 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 170 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 166 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.022789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.018601 restraints weight = 162996.878| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 4.76 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15119 Z= 0.220 Angle : 0.626 9.723 20518 Z= 0.305 Chirality : 0.043 0.156 2279 Planarity : 0.004 0.043 2624 Dihedral : 5.895 51.370 2110 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.38 % Allowed : 4.37 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.21), residues: 1849 helix: 1.26 (0.18), residues: 813 sheet: -0.40 (0.31), residues: 305 loop : 0.78 (0.26), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 183 TYR 0.009 0.001 TYR E 294 PHE 0.010 0.001 PHE A 262 TRP 0.016 0.002 TRP D 79 HIS 0.004 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00471 (15119) covalent geometry : angle 0.62601 (20518) hydrogen bonds : bond 0.03228 ( 707) hydrogen bonds : angle 5.03587 ( 1848) *********************** 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 93 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 132 MET cc_start: 0.8586 (tmm) cc_final: 0.8381 (tmm) REVERT: C 227 MET cc_start: 0.9285 (tpp) cc_final: 0.8875 (mmm) REVERT: C 269 MET cc_start: 0.9082 (tpp) cc_final: 0.8710 (mtt) REVERT: A 44 MET cc_start: -0.2799 (pmm) cc_final: -0.3205 (ptp) REVERT: A 82 MET cc_start: 0.9480 (tpt) cc_final: 0.9233 (tpt) REVERT: A 119 MET cc_start: 0.9393 (mtm) cc_final: 0.9179 (mtm) REVERT: A 176 MET cc_start: 0.8352 (mtp) cc_final: 0.8049 (mtm) REVERT: A 299 MET cc_start: 0.9115 (mtp) cc_final: 0.8740 (ptp) REVERT: A 305 MET cc_start: 0.8969 (mmm) cc_final: 0.8705 (mmm) REVERT: A 355 MET cc_start: 0.9430 (mmm) cc_final: 0.8713 (mpp) REVERT: A 375 PHE cc_start: 0.8081 (m-80) cc_final: 0.7854 (m-10) REVERT: E 47 MET cc_start: 0.2927 (ptm) cc_final: 0.1567 (mtt) REVERT: E 82 MET cc_start: 0.9170 (tpp) cc_final: 0.8778 (tpp) REVERT: E 132 MET cc_start: 0.8777 (tmm) cc_final: 0.8408 (tmm) REVERT: E 269 MET cc_start: 0.9278 (tpp) cc_final: 0.8717 (mtt) REVERT: B 82 MET cc_start: 0.9428 (tpt) cc_final: 0.8915 (tpt) REVERT: B 227 MET cc_start: 0.9291 (mmm) cc_final: 0.9047 (mmm) REVERT: D 44 MET cc_start: 0.8903 (tpp) cc_final: 0.8448 (tpp) REVERT: D 176 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8170 (mpp) REVERT: D 299 MET cc_start: 0.8886 (mtp) cc_final: 0.8594 (mmt) outliers start: 6 outliers final: 0 residues processed: 91 average time/residue: 0.1102 time to fit residues: 16.1574 Evaluate side-chains 88 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 3 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.2805 r_free = 0.2805 target = 0.023111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.018894 restraints weight = 159472.241| |-----------------------------------------------------------------------------| r_work (start): 0.2571 rms_B_bonded: 4.77 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15119 Z= 0.167 Angle : 0.601 9.744 20518 Z= 0.288 Chirality : 0.042 0.130 2279 Planarity : 0.004 0.043 2624 Dihedral : 5.686 46.884 2110 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.25 % Allowed : 5.38 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.21), residues: 1849 helix: 1.41 (0.19), residues: 818 sheet: -0.26 (0.31), residues: 295 loop : 0.76 (0.26), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.008 0.001 TYR D 188 PHE 0.009 0.001 PHE C 375 TRP 0.013 0.002 TRP E 79 HIS 0.003 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00363 (15119) covalent geometry : angle 0.60077 (20518) hydrogen bonds : bond 0.03046 ( 707) hydrogen bonds : angle 4.85505 ( 1848) *********************** 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 91 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: C 227 MET cc_start: 0.9265 (tpp) cc_final: 0.8946 (mmm) REVERT: C 269 MET cc_start: 0.9099 (tpp) cc_final: 0.8710 (mtt) REVERT: A 44 MET cc_start: -0.3586 (pmm) cc_final: -0.3908 (ptp) REVERT: A 82 MET cc_start: 0.9458 (tpt) cc_final: 0.9178 (tpt) REVERT: A 119 MET cc_start: 0.9381 (mtm) cc_final: 0.9166 (mtm) REVERT: A 227 MET cc_start: 0.9177 (mmm) cc_final: 0.8956 (mmm) REVERT: A 269 MET cc_start: 0.9175 (tpp) cc_final: 0.8814 (tpp) REVERT: A 299 MET cc_start: 0.9059 (mtp) cc_final: 0.8698 (ptp) REVERT: A 305 MET cc_start: 0.8994 (mmm) cc_final: 0.8714 (mmm) REVERT: A 355 MET cc_start: 0.9451 (mmm) cc_final: 0.8738 (mpp) REVERT: A 375 PHE cc_start: 0.7976 (m-80) cc_final: 0.7736 (m-10) REVERT: E 47 MET cc_start: 0.3092 (ptm) cc_final: 0.1421 (mtt) REVERT: E 132 MET cc_start: 0.8779 (tmm) cc_final: 0.8357 (tmm) REVERT: E 269 MET cc_start: 0.9241 (tpp) cc_final: 0.8743 (mtt) REVERT: B 82 MET cc_start: 0.9374 (tpt) cc_final: 0.9089 (tpt) REVERT: B 176 MET cc_start: 0.9082 (mtt) cc_final: 0.8860 (mtt) REVERT: B 227 MET cc_start: 0.9271 (mmm) cc_final: 0.8967 (mmm) REVERT: B 355 MET cc_start: 0.9361 (mmm) cc_final: 0.9155 (mpp) REVERT: D 44 MET cc_start: 0.8876 (tpp) cc_final: 0.8559 (tpp) REVERT: D 132 MET cc_start: 0.8698 (tmm) cc_final: 0.8343 (tmm) REVERT: D 176 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8156 (mpp) REVERT: D 283 MET cc_start: 0.9226 (mmm) cc_final: 0.8999 (mmm) outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 0.1054 time to fit residues: 15.2372 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 : 0.580 ------------------------------------------------------------------------------- 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 176 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 179 optimal weight: 0.1980 chunk 46 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 182 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.022717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.018566 restraints weight = 159486.086| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 4.70 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15119 Z= 0.191 Angle : 0.618 10.838 20518 Z= 0.294 Chirality : 0.042 0.128 2279 Planarity : 0.004 0.045 2624 Dihedral : 5.641 47.158 2110 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.32 % Allowed : 5.83 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.21), residues: 1849 helix: 1.43 (0.19), residues: 818 sheet: -0.25 (0.31), residues: 295 loop : 0.75 (0.26), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 290 TYR 0.008 0.001 TYR B 294 PHE 0.008 0.001 PHE F 29 TRP 0.015 0.002 TRP D 79 HIS 0.003 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00414 (15119) covalent geometry : angle 0.61814 (20518) hydrogen bonds : bond 0.03025 ( 707) hydrogen bonds : angle 4.83933 ( 1848) *********************** 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 92 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.625 Fit side-chains REVERT: C 82 MET cc_start: 0.9299 (tpt) cc_final: 0.8972 (tpt) REVERT: C 227 MET cc_start: 0.9288 (tpp) cc_final: 0.8950 (mmm) REVERT: C 269 MET cc_start: 0.9098 (tpp) cc_final: 0.8704 (mtt) REVERT: A 44 MET cc_start: -0.3919 (pmm) cc_final: -0.4173 (ptp) REVERT: A 82 MET cc_start: 0.9481 (tpt) cc_final: 0.9056 (tpt) REVERT: A 119 MET cc_start: 0.9403 (mtm) cc_final: 0.9172 (mtm) REVERT: A 227 MET cc_start: 0.9173 (mmm) cc_final: 0.8930 (mmm) REVERT: A 269 MET cc_start: 0.9212 (tpp) cc_final: 0.8847 (tpp) REVERT: A 299 MET cc_start: 0.9112 (mtp) cc_final: 0.8653 (ptp) REVERT: A 305 MET cc_start: 0.9025 (mmm) cc_final: 0.8722 (mmm) REVERT: A 355 MET cc_start: 0.9444 (mmm) cc_final: 0.8770 (mpp) REVERT: A 375 PHE cc_start: 0.8058 (m-80) cc_final: 0.7808 (m-10) REVERT: E 269 MET cc_start: 0.9268 (tpp) cc_final: 0.8747 (mtt) REVERT: B 82 MET cc_start: 0.9394 (tpt) cc_final: 0.9059 (tpt) REVERT: B 227 MET cc_start: 0.9298 (mmm) cc_final: 0.9049 (mmm) REVERT: B 355 MET cc_start: 0.9320 (mmm) cc_final: 0.9087 (mpp) REVERT: D 44 MET cc_start: 0.8884 (tpp) cc_final: 0.8549 (tpp) REVERT: D 132 MET cc_start: 0.8699 (tmm) cc_final: 0.8380 (tmm) REVERT: D 176 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8208 (mpp) outliers start: 5 outliers final: 3 residues processed: 90 average time/residue: 0.1170 time to fit residues: 16.9034 Evaluate side-chains 90 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 176 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 153 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.022960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.018777 restraints weight = 157459.616| |-----------------------------------------------------------------------------| r_work (start): 0.2570 rms_B_bonded: 4.73 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15119 Z= 0.168 Angle : 0.622 11.748 20518 Z= 0.293 Chirality : 0.042 0.131 2279 Planarity : 0.004 0.045 2624 Dihedral : 5.559 49.591 2110 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.32 % Allowed : 6.40 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.21), residues: 1849 helix: 1.48 (0.19), residues: 818 sheet: -0.21 (0.31), residues: 295 loop : 0.74 (0.26), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.010 0.001 TYR C 169 PHE 0.010 0.001 PHE C 375 TRP 0.013 0.002 TRP D 79 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00366 (15119) covalent geometry : angle 0.62154 (20518) hydrogen bonds : bond 0.02955 ( 707) hydrogen bonds : angle 4.78569 ( 1848) *********************** 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 91 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.609 Fit side-chains REVERT: C 82 MET cc_start: 0.9299 (tpt) cc_final: 0.9068 (tpt) REVERT: C 119 MET cc_start: 0.9429 (mtp) cc_final: 0.9085 (mtt) REVERT: C 227 MET cc_start: 0.9275 (tpp) cc_final: 0.8933 (mmm) REVERT: C 269 MET cc_start: 0.9101 (tpp) cc_final: 0.8685 (mtt) REVERT: C 305 MET cc_start: 0.9268 (mmm) cc_final: 0.8805 (mmm) REVERT: A 44 MET cc_start: -0.4145 (pmm) cc_final: -0.4457 (ptp) REVERT: A 82 MET cc_start: 0.9466 (tpt) cc_final: 0.9056 (tpt) REVERT: A 227 MET cc_start: 0.9180 (mmm) cc_final: 0.8921 (mmm) REVERT: A 299 MET cc_start: 0.9076 (mtp) cc_final: 0.8696 (ptp) REVERT: A 305 MET cc_start: 0.9081 (mmm) cc_final: 0.8859 (mmm) REVERT: A 355 MET cc_start: 0.9455 (mmm) cc_final: 0.8807 (mpp) REVERT: A 375 PHE cc_start: 0.7945 (m-80) cc_final: 0.7688 (m-10) REVERT: E 44 MET cc_start: 0.8926 (mtp) cc_final: 0.8703 (mtp) REVERT: E 47 MET cc_start: 0.3523 (ptp) cc_final: 0.0417 (tpp) REVERT: E 269 MET cc_start: 0.9250 (tpp) cc_final: 0.8775 (mtt) REVERT: B 82 MET cc_start: 0.9389 (tpt) cc_final: 0.9006 (tpt) REVERT: B 227 MET cc_start: 0.9278 (mmm) cc_final: 0.9026 (mmm) REVERT: B 355 MET cc_start: 0.9341 (mmm) cc_final: 0.9086 (mpp) REVERT: D 44 MET cc_start: 0.8892 (tpp) cc_final: 0.8571 (tpp) REVERT: D 132 MET cc_start: 0.8717 (tmm) cc_final: 0.8417 (tmm) REVERT: D 176 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8182 (mpp) outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 0.1049 time to fit residues: 15.3707 Evaluate side-chains 90 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 176 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 184 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.023031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.018837 restraints weight = 156401.966| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 4.73 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15119 Z= 0.169 Angle : 0.636 12.167 20518 Z= 0.297 Chirality : 0.042 0.138 2279 Planarity : 0.004 0.045 2624 Dihedral : 5.514 52.239 2110 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.38 % Allowed : 6.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.21), residues: 1849 helix: 1.48 (0.19), residues: 818 sheet: -0.20 (0.31), residues: 295 loop : 0.73 (0.26), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 32 TYR 0.008 0.001 TYR A 143 PHE 0.007 0.001 PHE A 262 TRP 0.014 0.002 TRP D 79 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00370 (15119) covalent geometry : angle 0.63618 (20518) hydrogen bonds : bond 0.02963 ( 707) hydrogen bonds : angle 4.74842 ( 1848) *********************** 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 92 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.638 Fit side-chains REVERT: C 82 MET cc_start: 0.9314 (tpt) cc_final: 0.9053 (tpt) REVERT: C 119 MET cc_start: 0.9411 (mtp) cc_final: 0.9075 (mtt) REVERT: C 227 MET cc_start: 0.9282 (tpp) cc_final: 0.8948 (mmm) REVERT: C 269 MET cc_start: 0.9108 (tpp) cc_final: 0.8682 (mtt) REVERT: C 305 MET cc_start: 0.9276 (mmm) cc_final: 0.8914 (mmm) REVERT: A 44 MET cc_start: -0.4247 (pmm) cc_final: -0.4478 (ptp) REVERT: A 82 MET cc_start: 0.9508 (tpt) cc_final: 0.9068 (tpt) REVERT: A 227 MET cc_start: 0.9181 (mmm) cc_final: 0.8911 (mmm) REVERT: A 269 MET cc_start: 0.9014 (tpp) cc_final: 0.8657 (tpp) REVERT: A 299 MET cc_start: 0.9067 (mtp) cc_final: 0.8693 (ptp) REVERT: A 305 MET cc_start: 0.9095 (mmm) cc_final: 0.8854 (mmm) REVERT: A 355 MET cc_start: 0.9446 (mmm) cc_final: 0.8792 (mpp) REVERT: A 375 PHE cc_start: 0.7889 (m-80) cc_final: 0.7619 (m-10) REVERT: E 47 MET cc_start: 0.3901 (ptp) cc_final: 0.1095 (tpp) REVERT: E 269 MET cc_start: 0.9254 (tpp) cc_final: 0.8795 (mtt) REVERT: B 82 MET cc_start: 0.9409 (tpt) cc_final: 0.9166 (tpt) REVERT: B 227 MET cc_start: 0.9282 (mmm) cc_final: 0.9027 (mmm) REVERT: B 305 MET cc_start: 0.9353 (mmm) cc_final: 0.9142 (mmm) REVERT: B 355 MET cc_start: 0.9317 (mmm) cc_final: 0.9083 (mpp) REVERT: D 44 MET cc_start: 0.8908 (tpp) cc_final: 0.8539 (tpp) REVERT: D 132 MET cc_start: 0.8734 (tmm) cc_final: 0.8437 (tmm) REVERT: D 176 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8186 (mpp) REVERT: D 283 MET cc_start: 0.9245 (mmm) cc_final: 0.9006 (mmm) outliers start: 6 outliers final: 4 residues processed: 89 average time/residue: 0.1091 time to fit residues: 15.9586 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 : 0.519 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 21 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 8 optimal weight: 0.0070 chunk 125 optimal weight: 0.8980 overall best weight: 1.7802 ------------------------------------------------------------------------------- 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** A 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.023435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.019255 restraints weight = 156426.236| |-----------------------------------------------------------------------------| r_work (start): 0.2588 rms_B_bonded: 4.76 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15119 Z= 0.110 Angle : 0.617 12.658 20518 Z= 0.284 Chirality : 0.042 0.141 2279 Planarity : 0.004 0.046 2624 Dihedral : 5.275 51.319 2110 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.44 % Allowed : 6.90 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.21), residues: 1849 helix: 1.42 (0.19), residues: 848 sheet: -0.15 (0.31), residues: 295 loop : 0.75 (0.26), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 62 TYR 0.008 0.001 TYR E 188 PHE 0.011 0.001 PHE C 375 TRP 0.014 0.002 TRP C 356 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00248 (15119) covalent geometry : angle 0.61730 (20518) hydrogen bonds : bond 0.02805 ( 707) hydrogen bonds : angle 4.61267 ( 1848) *********************** 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 94 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.628 Fit side-chains REVERT: C 82 MET cc_start: 0.9326 (tpt) cc_final: 0.9047 (tpt) REVERT: C 227 MET cc_start: 0.9239 (tpp) cc_final: 0.8930 (mmm) REVERT: C 269 MET cc_start: 0.9124 (tpp) cc_final: 0.8686 (mtt) REVERT: C 305 MET cc_start: 0.9255 (mmm) cc_final: 0.8919 (mmm) REVERT: A 44 MET cc_start: -0.4084 (OUTLIER) cc_final: -0.4295 (ptp) REVERT: A 82 MET cc_start: 0.9528 (tpt) cc_final: 0.9128 (tpt) REVERT: A 227 MET cc_start: 0.9169 (mmm) cc_final: 0.8888 (mmm) REVERT: A 269 MET cc_start: 0.9017 (tpp) cc_final: 0.8653 (tpp) REVERT: A 305 MET cc_start: 0.9124 (mmm) cc_final: 0.8867 (mmm) REVERT: A 355 MET cc_start: 0.9441 (mmm) cc_final: 0.8811 (mpp) REVERT: E 132 MET cc_start: 0.9064 (tmm) cc_final: 0.8838 (tmm) REVERT: E 269 MET cc_start: 0.9241 (tpp) cc_final: 0.8824 (mtt) REVERT: B 82 MET cc_start: 0.9369 (tpt) cc_final: 0.9113 (tpt) REVERT: B 227 MET cc_start: 0.9223 (mmm) cc_final: 0.8951 (mmm) REVERT: B 325 MET cc_start: 0.9089 (mmm) cc_final: 0.8762 (mmm) REVERT: B 355 MET cc_start: 0.9312 (mmm) cc_final: 0.9076 (mpp) REVERT: D 44 MET cc_start: 0.8898 (tpp) cc_final: 0.8534 (tpp) REVERT: D 176 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8173 (mpp) REVERT: D 227 MET cc_start: 0.9284 (mmm) cc_final: 0.8982 (mmm) REVERT: D 283 MET cc_start: 0.9287 (mmm) cc_final: 0.9082 (mmm) outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.0994 time to fit residues: 14.6681 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 : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET 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 176 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 135 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.022986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.018799 restraints weight = 158278.293| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 4.71 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15119 Z= 0.267 Angle : 0.706 13.120 20518 Z= 0.331 Chirality : 0.043 0.142 2279 Planarity : 0.004 0.045 2624 Dihedral : 5.616 58.052 2110 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.21), residues: 1849 helix: 1.45 (0.19), residues: 818 sheet: -0.22 (0.31), residues: 295 loop : 0.70 (0.26), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 32 TYR 0.009 0.001 TYR A 143 PHE 0.011 0.001 PHE F 29 TRP 0.016 0.002 TRP E 79 HIS 0.005 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00570 (15119) covalent geometry : angle 0.70635 (20518) hydrogen bonds : bond 0.03178 ( 707) hydrogen bonds : angle 4.90441 ( 1848) ********************** 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 89 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.568 Fit side-chains REVERT: C 82 MET cc_start: 0.9349 (tpt) cc_final: 0.8782 (tpp) REVERT: C 269 MET cc_start: 0.9141 (tpp) cc_final: 0.8720 (mtt) REVERT: C 305 MET cc_start: 0.9278 (mmm) cc_final: 0.8923 (mmm) REVERT: A 44 MET cc_start: -0.3953 (OUTLIER) cc_final: -0.4232 (ptp) REVERT: A 82 MET cc_start: 0.9481 (tpt) cc_final: 0.9068 (tpt) REVERT: A 227 MET cc_start: 0.9241 (mmm) cc_final: 0.8965 (mmm) REVERT: A 269 MET cc_start: 0.9121 (tpp) cc_final: 0.8753 (tpp) REVERT: A 283 MET cc_start: 0.9582 (mmp) cc_final: 0.9328 (mmm) REVERT: A 305 MET cc_start: 0.9086 (mmm) cc_final: 0.8870 (mmm) REVERT: A 355 MET cc_start: 0.9443 (mmm) cc_final: 0.8760 (mpp) REVERT: E 269 MET cc_start: 0.9270 (tpp) cc_final: 0.8766 (mtt) REVERT: B 82 MET cc_start: 0.9367 (tpt) cc_final: 0.9105 (tpt) REVERT: B 227 MET cc_start: 0.9327 (mmm) cc_final: 0.8998 (mmm) REVERT: B 355 MET cc_start: 0.9356 (mmm) cc_final: 0.9132 (mmm) REVERT: D 44 MET cc_start: 0.8883 (tpp) cc_final: 0.8530 (tpp) REVERT: D 176 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8173 (mpp) REVERT: D 283 MET cc_start: 0.9261 (mmm) cc_final: 0.9038 (mmm) outliers start: 5 outliers final: 3 residues processed: 86 average time/residue: 0.1090 time to fit residues: 15.3302 Evaluate side-chains 88 residues out of total 1579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET 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 176 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 59 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.023252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.019073 restraints weight = 156126.192| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 4.70 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15119 Z= 0.200 Angle : 0.662 12.910 20518 Z= 0.309 Chirality : 0.043 0.143 2279 Planarity : 0.004 0.045 2624 Dihedral : 5.596 57.853 2110 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.21), residues: 1849 helix: 1.48 (0.19), residues: 818 sheet: -0.21 (0.31), residues: 295 loop : 0.69 (0.26), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 32 TYR 0.007 0.001 TYR A 169 PHE 0.011 0.001 PHE C 375 TRP 0.015 0.002 TRP E 79 HIS 0.003 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00435 (15119) covalent geometry : angle 0.66210 (20518) hydrogen bonds : bond 0.03077 ( 707) hydrogen bonds : angle 4.80245 ( 1848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.41 seconds wall clock time: 37 minutes 3.14 seconds (2223.14 seconds total)