Starting phenix.real_space_refine on Sat Aug 23 21:33:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gob_51496/08_2025/9gob_51496.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gob_51496/08_2025/9gob_51496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gob_51496/08_2025/9gob_51496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gob_51496/08_2025/9gob_51496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gob_51496/08_2025/9gob_51496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gob_51496/08_2025/9gob_51496.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.065 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 106 5.16 5 C 9343 2.51 5 N 2506 2.21 5 O 2844 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14814 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: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 174 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} 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: 3.38, per 1000 atoms: 0.23 Number of scatterers: 14814 At special positions: 0 Unit cell: (99.84, 78, 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 106 16.00 P 10 15.00 Mg 5 11.99 O 2844 8.00 N 2506 7.00 C 9343 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 649.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3476 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 25 sheets defined 52.4% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.690A 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: 3.773A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.525A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.525A 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: 3.661A 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: 3.532A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.650A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 3.552A 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: 3.789A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 40 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.693A 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: 3.780A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.857A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 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: 3.669A 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: 3.621A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.545A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.723A 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: 3.771A 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: 3.681A 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: 3.778A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.504A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 3.687A 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: 3.646A 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: 3.626A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.590A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 3.757A 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: 3.776A 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: 3.704A 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: 3.789A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.519A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 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: 3.656A 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: 3.652A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.540A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.722A 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: 3.845A 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: 3.686A 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: 3.778A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.514A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (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: 3.662A 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 removed outlier: 3.506A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) 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: 3.635A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.567A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.737A 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: 3.781A 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: 6.736A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 7.981A 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: 3.670A 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: 6.621A 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: 6.850A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.035A 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: 3.836A 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: 6.308A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.621A 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: 6.912A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.059A 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 removed outlier: 3.561A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) 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: 6.286A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.566A 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: 6.845A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.078A 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: 3.534A 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: 6.625A 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: 6.831A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.330A 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: 3.573A 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: 6.603A 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 241 708 hydrogen bonds defined for protein. 1842 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: 2.73 Time building geometry restraints manager: 1.18 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: 4831 1.34 - 1.46: 3010 1.46 - 1.58: 7093 1.58 - 1.69: 15 1.69 - 1.81: 186 Bond restraints: 15135 Sorted by residual: bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.21e+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 1.18e+00 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 1.16e+00 bond pdb=" CA GLU D 334 " pdb=" CB GLU D 334 " ideal model delta sigma weight residual 1.533 1.551 -0.018 1.66e-02 3.63e+03 1.14e+00 ... (remaining 15130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 19925 1.79 - 3.59: 522 3.59 - 5.38: 63 5.38 - 7.18: 20 7.18 - 8.97: 10 Bond angle restraints: 20540 Sorted by residual: angle pdb=" CA GLU B 334 " pdb=" CB GLU B 334 " pdb=" CG GLU B 334 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CA GLU A 334 " pdb=" CB GLU A 334 " pdb=" CG GLU A 334 " ideal model delta sigma weight residual 114.10 120.98 -6.88 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CA GLU E 334 " pdb=" CB GLU E 334 " pdb=" CG GLU E 334 " ideal model delta sigma weight residual 114.10 120.96 -6.86 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CA GLU D 334 " pdb=" CB GLU D 334 " pdb=" CG GLU D 334 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.16e+01 angle pdb=" N GLY A 182 " pdb=" CA GLY A 182 " pdb=" C GLY A 182 " ideal model delta sigma weight residual 113.27 117.72 -4.45 1.33e+00 5.65e-01 1.12e+01 ... (remaining 20535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.03: 8584 20.03 - 40.07: 432 40.07 - 60.10: 61 60.10 - 80.13: 17 80.13 - 100.17: 11 Dihedral angle restraints: 9105 sinusoidal: 3676 harmonic: 5429 Sorted by residual: dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 40.17 -100.17 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 40.07 -100.07 1 2.00e+01 2.50e-03 2.82e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 40.02 -100.02 1 2.00e+01 2.50e-03 2.82e+01 ... (remaining 9102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1572 0.044 - 0.087: 524 0.087 - 0.131: 151 0.131 - 0.175: 31 0.175 - 0.218: 5 Chirality restraints: 2283 Sorted by residual: chirality pdb=" CA GLU B 334 " pdb=" N GLU B 334 " pdb=" C GLU B 334 " pdb=" CB GLU B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+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 1.18e+00 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 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2280 not shown) Planarity restraints: 2626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 183 " -0.255 9.50e-02 1.11e+02 1.15e-01 1.06e+01 pdb=" NE ARG B 183 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 183 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG B 183 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 183 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 183 " -0.259 9.50e-02 1.11e+02 1.17e-01 1.05e+01 pdb=" NE ARG C 183 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG C 183 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG C 183 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 183 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 183 " -0.258 9.50e-02 1.11e+02 1.16e-01 1.04e+01 pdb=" NE ARG D 183 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG D 183 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG D 183 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG D 183 " -0.001 2.00e-02 2.50e+03 ... (remaining 2623 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 90 2.54 - 3.13: 11865 3.13 - 3.72: 22966 3.72 - 4.31: 34590 4.31 - 4.90: 56579 Nonbonded interactions: 126090 Sorted by model distance: nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 1.947 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.970 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.974 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.976 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 2.006 2.170 ... (remaining 126085 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.160 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 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 : 0.008 0.873 15136 Z= 0.723 Angle : 0.732 8.973 20540 Z= 0.408 Chirality : 0.048 0.218 2283 Planarity : 0.011 0.117 2626 Dihedral : 13.184 100.167 5629 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: -1.88 (0.17), residues: 1852 helix: -1.84 (0.14), residues: 809 sheet: -1.09 (0.29), residues: 305 loop : -0.26 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.005 ARG B 183 TYR 0.016 0.004 TYR D 188 PHE 0.008 0.001 PHE E 127 TRP 0.025 0.004 TRP E 86 HIS 0.003 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00307 (15135) covalent geometry : angle 0.73248 (20540) hydrogen bonds : bond 0.14462 ( 708) hydrogen bonds : angle 7.46758 ( 1842) Misc. bond : bond 0.87298 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 313 MET cc_start: 0.8853 (tpp) cc_final: 0.8579 (tpt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1356 time to fit residues: 23.0761 Evaluate side-chains 87 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 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** ** D 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 = 0.2803 r_free = 0.2803 target = 0.029400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.023761 restraints weight = 100444.751| |-----------------------------------------------------------------------------| r_work (start): 0.2536 rms_B_bonded: 3.70 r_work: 0.2394 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 15136 Z= 0.311 Angle : 0.726 7.819 20540 Z= 0.363 Chirality : 0.046 0.176 2283 Planarity : 0.005 0.045 2626 Dihedral : 7.170 75.069 2112 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.06 % Allowed : 2.28 % Favored : 97.66 % 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: 0.05 (0.20), residues: 1852 helix: 0.12 (0.18), residues: 819 sheet: -0.66 (0.29), residues: 315 loop : 0.59 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 95 TYR 0.013 0.001 TYR B 294 PHE 0.015 0.001 PHE E 375 TRP 0.017 0.002 TRP C 79 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00683 (15135) covalent geometry : angle 0.72577 (20540) hydrogen bonds : bond 0.04068 ( 708) hydrogen bonds : angle 5.74261 ( 1842) Misc. bond : bond 0.00091 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.608 Fit side-chains REVERT: C 44 MET cc_start: 0.9228 (ttm) cc_final: 0.8966 (tpp) REVERT: C 227 MET cc_start: 0.9462 (tpt) cc_final: 0.9086 (tpt) REVERT: C 269 MET cc_start: 0.9180 (tpp) cc_final: 0.8854 (ttm) REVERT: C 305 MET cc_start: 0.9440 (mmm) cc_final: 0.9223 (mmm) REVERT: F 32 ARG cc_start: 0.8435 (tmm-80) cc_final: 0.8201 (tmm-80) REVERT: A 10 CYS cc_start: 0.8866 (t) cc_final: 0.8442 (t) REVERT: A 44 MET cc_start: -0.1012 (pmm) cc_final: -0.1876 (ptp) REVERT: A 269 MET cc_start: 0.8955 (tpp) cc_final: 0.8511 (mtt) REVERT: A 283 MET cc_start: 0.9438 (mmm) cc_final: 0.9175 (mmm) REVERT: A 355 MET cc_start: 0.9413 (mmp) cc_final: 0.9202 (mmp) REVERT: E 119 MET cc_start: 0.9625 (mtm) cc_final: 0.9339 (mtp) REVERT: E 123 MET cc_start: 0.9627 (mmm) cc_final: 0.9413 (mmp) REVERT: E 313 MET cc_start: 0.9604 (tpp) cc_final: 0.9132 (tpt) REVERT: E 355 MET cc_start: 0.9528 (mmp) cc_final: 0.9189 (mmm) REVERT: B 227 MET cc_start: 0.9577 (tpt) cc_final: 0.9091 (tpp) REVERT: B 313 MET cc_start: 0.9781 (tpp) cc_final: 0.9223 (mmm) REVERT: B 355 MET cc_start: 0.9562 (mmm) cc_final: 0.9259 (mmp) REVERT: D 82 MET cc_start: 0.9554 (tpt) cc_final: 0.9334 (tpt) REVERT: D 269 MET cc_start: 0.9486 (tpp) cc_final: 0.8920 (mtp) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.0977 time to fit residues: 13.6414 Evaluate side-chains 86 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 59 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 164 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS ** D 115 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 = 0.2841 r_free = 0.2841 target = 0.030474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.024895 restraints weight = 97514.570| |-----------------------------------------------------------------------------| r_work (start): 0.2582 rms_B_bonded: 3.79 r_work: 0.2437 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15136 Z= 0.111 Angle : 0.570 8.766 20540 Z= 0.281 Chirality : 0.042 0.138 2283 Planarity : 0.004 0.048 2626 Dihedral : 5.891 52.087 2112 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % 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: 0.95 (0.21), residues: 1852 helix: 0.94 (0.19), residues: 824 sheet: -0.27 (0.31), residues: 295 loop : 0.95 (0.26), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 95 TYR 0.011 0.001 TYR C 143 PHE 0.004 0.001 PHE D 223 TRP 0.010 0.001 TRP D 340 HIS 0.002 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00246 (15135) covalent geometry : angle 0.57020 (20540) hydrogen bonds : bond 0.03246 ( 708) hydrogen bonds : angle 5.06324 ( 1842) Misc. bond : bond 0.00102 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.601 Fit side-chains REVERT: C 44 MET cc_start: 0.9104 (ttm) cc_final: 0.8808 (tpt) REVERT: C 82 MET cc_start: 0.9332 (tpp) cc_final: 0.9014 (tpt) REVERT: C 227 MET cc_start: 0.9429 (tpt) cc_final: 0.9068 (tpt) REVERT: C 269 MET cc_start: 0.9017 (tpp) cc_final: 0.8759 (ttm) REVERT: C 305 MET cc_start: 0.9441 (mmm) cc_final: 0.9209 (mmm) REVERT: C 355 MET cc_start: 0.9563 (mmm) cc_final: 0.9299 (mmp) REVERT: A 10 CYS cc_start: 0.8510 (t) cc_final: 0.8227 (t) REVERT: A 44 MET cc_start: -0.1702 (pmm) cc_final: -0.2254 (ptp) REVERT: A 269 MET cc_start: 0.8881 (tpp) cc_final: 0.8438 (mtt) REVERT: A 283 MET cc_start: 0.9468 (mmm) cc_final: 0.9248 (mmm) REVERT: E 82 MET cc_start: 0.9559 (tpt) cc_final: 0.9274 (tpt) REVERT: E 305 MET cc_start: 0.9459 (mmm) cc_final: 0.9226 (mmm) REVERT: E 313 MET cc_start: 0.9548 (tpp) cc_final: 0.9074 (tpt) REVERT: B 123 MET cc_start: 0.9575 (mmm) cc_final: 0.9305 (mmp) REVERT: B 227 MET cc_start: 0.9589 (tpt) cc_final: 0.9282 (mmm) REVERT: B 269 MET cc_start: 0.9278 (tpp) cc_final: 0.8907 (mtp) REVERT: B 305 MET cc_start: 0.9537 (mmm) cc_final: 0.9332 (mmm) REVERT: B 313 MET cc_start: 0.9757 (tpp) cc_final: 0.9212 (mmm) REVERT: B 355 MET cc_start: 0.9579 (mmm) cc_final: 0.9289 (mmp) REVERT: D 269 MET cc_start: 0.9441 (tpp) cc_final: 0.9021 (mtp) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.0940 time to fit residues: 13.3926 Evaluate side-chains 87 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 47 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.2802 r_free = 0.2802 target = 0.029439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.023784 restraints weight = 99279.584| |-----------------------------------------------------------------------------| r_work (start): 0.2532 rms_B_bonded: 3.80 r_work: 0.2384 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15136 Z= 0.198 Angle : 0.599 7.701 20540 Z= 0.292 Chirality : 0.043 0.143 2283 Planarity : 0.004 0.049 2626 Dihedral : 5.721 45.314 2112 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.25 % Allowed : 3.92 % Favored : 95.82 % 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: 1.15 (0.21), residues: 1852 helix: 1.25 (0.19), residues: 824 sheet: -0.33 (0.31), residues: 305 loop : 0.96 (0.26), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 95 TYR 0.009 0.001 TYR C 143 PHE 0.008 0.001 PHE A 375 TRP 0.013 0.002 TRP C 79 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00438 (15135) covalent geometry : angle 0.59876 (20540) hydrogen bonds : bond 0.03289 ( 708) hydrogen bonds : angle 4.99272 ( 1842) Misc. bond : bond 0.00087 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.455 Fit side-chains REVERT: C 82 MET cc_start: 0.9345 (tpp) cc_final: 0.9019 (tpt) REVERT: C 227 MET cc_start: 0.9504 (tpt) cc_final: 0.9144 (tpp) REVERT: C 269 MET cc_start: 0.9113 (tpp) cc_final: 0.8662 (ttm) REVERT: C 305 MET cc_start: 0.9459 (mmm) cc_final: 0.9205 (mmm) REVERT: C 355 MET cc_start: 0.9589 (mmm) cc_final: 0.9301 (mmp) REVERT: A 10 CYS cc_start: 0.8575 (t) cc_final: 0.8304 (t) REVERT: A 82 MET cc_start: 0.9582 (tpt) cc_final: 0.9321 (tpt) REVERT: A 269 MET cc_start: 0.8941 (tpp) cc_final: 0.8503 (mtt) REVERT: A 299 MET cc_start: 0.9171 (ttp) cc_final: 0.8912 (ttm) REVERT: A 313 MET cc_start: 0.9820 (tpp) cc_final: 0.9324 (tpp) REVERT: A 355 MET cc_start: 0.9396 (mmp) cc_final: 0.9174 (mmp) REVERT: A 375 PHE cc_start: 0.7545 (m-80) cc_final: 0.7290 (m-80) REVERT: E 47 MET cc_start: 0.7013 (ppp) cc_final: 0.6484 (ppp) REVERT: E 119 MET cc_start: 0.9351 (mtp) cc_final: 0.9129 (mtp) REVERT: E 132 MET cc_start: 0.9259 (tmm) cc_final: 0.9041 (tmm) REVERT: E 313 MET cc_start: 0.9577 (tpp) cc_final: 0.9103 (tpt) REVERT: E 355 MET cc_start: 0.9518 (mmp) cc_final: 0.9229 (mmm) REVERT: E 375 PHE cc_start: 0.7959 (t80) cc_final: 0.7306 (t80) REVERT: B 227 MET cc_start: 0.9587 (tpt) cc_final: 0.9275 (mmm) REVERT: B 269 MET cc_start: 0.9344 (tpp) cc_final: 0.8858 (mtp) REVERT: B 305 MET cc_start: 0.9528 (mmm) cc_final: 0.9298 (mmm) REVERT: B 313 MET cc_start: 0.9769 (tpp) cc_final: 0.9205 (mmm) REVERT: B 355 MET cc_start: 0.9588 (mmm) cc_final: 0.9283 (mmp) REVERT: D 227 MET cc_start: 0.9210 (mmm) cc_final: 0.8968 (mmm) REVERT: D 269 MET cc_start: 0.9467 (tpp) cc_final: 0.8984 (mtp) outliers start: 4 outliers final: 1 residues processed: 89 average time/residue: 0.0825 time to fit residues: 12.1176 Evaluate side-chains 85 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 18 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.2812 r_free = 0.2812 target = 0.029693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.024010 restraints weight = 99018.752| |-----------------------------------------------------------------------------| r_work (start): 0.2541 rms_B_bonded: 3.85 r_work: 0.2393 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15136 Z= 0.158 Angle : 0.600 12.684 20540 Z= 0.284 Chirality : 0.042 0.155 2283 Planarity : 0.004 0.049 2626 Dihedral : 5.533 40.598 2112 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.32 % Allowed : 4.24 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.21), residues: 1852 helix: 1.41 (0.19), residues: 824 sheet: -0.34 (0.31), residues: 305 loop : 1.00 (0.26), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 290 TYR 0.008 0.001 TYR C 143 PHE 0.007 0.001 PHE C 262 TRP 0.012 0.002 TRP C 79 HIS 0.002 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00352 (15135) covalent geometry : angle 0.59967 (20540) hydrogen bonds : bond 0.03178 ( 708) hydrogen bonds : angle 4.82717 ( 1842) Misc. bond : bond 0.00078 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.435 Fit side-chains REVERT: C 82 MET cc_start: 0.9333 (tpp) cc_final: 0.9010 (tpt) REVERT: C 227 MET cc_start: 0.9501 (tpt) cc_final: 0.9126 (tpp) REVERT: C 269 MET cc_start: 0.9080 (tpp) cc_final: 0.8848 (ttm) REVERT: C 305 MET cc_start: 0.9453 (mmm) cc_final: 0.9209 (mmm) REVERT: C 355 MET cc_start: 0.9595 (mmm) cc_final: 0.9283 (mmp) REVERT: A 10 CYS cc_start: 0.8584 (t) cc_final: 0.8349 (t) REVERT: A 82 MET cc_start: 0.9675 (tpt) cc_final: 0.9170 (tpp) REVERT: A 269 MET cc_start: 0.8906 (tpp) cc_final: 0.8472 (mtt) REVERT: A 299 MET cc_start: 0.9179 (ttp) cc_final: 0.8926 (ttm) REVERT: A 375 PHE cc_start: 0.7552 (m-80) cc_final: 0.7282 (m-80) REVERT: E 47 MET cc_start: 0.6846 (ppp) cc_final: 0.6046 (ppp) REVERT: E 283 MET cc_start: 0.9385 (mmm) cc_final: 0.9123 (mmm) REVERT: E 313 MET cc_start: 0.9559 (tpp) cc_final: 0.9074 (tpt) REVERT: E 355 MET cc_start: 0.9501 (mmp) cc_final: 0.9236 (mmm) REVERT: B 132 MET cc_start: 0.9392 (tmm) cc_final: 0.9041 (tmm) REVERT: B 227 MET cc_start: 0.9580 (tpt) cc_final: 0.9263 (mmm) REVERT: B 269 MET cc_start: 0.9317 (tpp) cc_final: 0.8829 (mtp) REVERT: B 305 MET cc_start: 0.9533 (mmm) cc_final: 0.9308 (mmm) REVERT: B 355 MET cc_start: 0.9576 (mmm) cc_final: 0.9258 (mmp) REVERT: D 269 MET cc_start: 0.9445 (tpp) cc_final: 0.9018 (mtp) outliers start: 5 outliers final: 3 residues processed: 90 average time/residue: 0.0783 time to fit residues: 11.4700 Evaluate side-chains 88 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain D residue 71 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 143 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 171 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.029094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.023597 restraints weight = 102252.710| |-----------------------------------------------------------------------------| r_work (start): 0.2529 rms_B_bonded: 3.61 r_work: 0.2394 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 15136 Z= 0.326 Angle : 0.685 10.662 20540 Z= 0.333 Chirality : 0.045 0.148 2283 Planarity : 0.004 0.046 2626 Dihedral : 5.939 54.129 2112 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.38 % Allowed : 4.30 % Favored : 95.32 % 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: 1852 helix: 1.40 (0.19), residues: 824 sheet: -0.62 (0.29), residues: 325 loop : 1.03 (0.27), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 290 TYR 0.009 0.001 TYR C 143 PHE 0.010 0.001 PHE C 21 TRP 0.017 0.002 TRP D 79 HIS 0.003 0.001 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00709 (15135) covalent geometry : angle 0.68495 (20540) hydrogen bonds : bond 0.03600 ( 708) hydrogen bonds : angle 5.10917 ( 1842) Misc. bond : bond 0.00092 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.361 Fit side-chains REVERT: C 44 MET cc_start: 0.9263 (tpp) cc_final: 0.8927 (mmm) REVERT: C 82 MET cc_start: 0.9345 (tpp) cc_final: 0.8891 (tmm) REVERT: C 269 MET cc_start: 0.9267 (tpp) cc_final: 0.8872 (ttm) REVERT: C 355 MET cc_start: 0.9580 (mmm) cc_final: 0.9279 (mmm) REVERT: A 10 CYS cc_start: 0.8635 (t) cc_final: 0.8321 (t) REVERT: A 82 MET cc_start: 0.9620 (tpt) cc_final: 0.9016 (tpp) REVERT: A 269 MET cc_start: 0.9018 (tpp) cc_final: 0.8679 (mtt) REVERT: A 375 PHE cc_start: 0.7686 (m-80) cc_final: 0.7409 (m-80) REVERT: E 47 MET cc_start: 0.7230 (ppp) cc_final: 0.6463 (ppp) REVERT: E 313 MET cc_start: 0.9509 (tpp) cc_final: 0.9052 (tpt) REVERT: E 355 MET cc_start: 0.9483 (mmp) cc_final: 0.9216 (mmm) REVERT: E 375 PHE cc_start: 0.7994 (t80) cc_final: 0.7793 (t80) REVERT: B 44 MET cc_start: 0.1107 (ptt) cc_final: 0.0626 (ptp) REVERT: B 123 MET cc_start: 0.9620 (mmt) cc_final: 0.9332 (mmp) REVERT: B 227 MET cc_start: 0.9583 (tpt) cc_final: 0.9264 (mmm) REVERT: B 269 MET cc_start: 0.9345 (tpp) cc_final: 0.8923 (mtp) REVERT: B 305 MET cc_start: 0.9562 (mmm) cc_final: 0.9331 (mmm) REVERT: B 355 MET cc_start: 0.9556 (mmm) cc_final: 0.9245 (mmp) REVERT: D 269 MET cc_start: 0.9502 (tpp) cc_final: 0.9050 (mtp) outliers start: 6 outliers final: 5 residues processed: 91 average time/residue: 0.0822 time to fit residues: 12.1277 Evaluate side-chains 91 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 133 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 186 optimal weight: 0.3980 chunk 48 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.2827 r_free = 0.2827 target = 0.030106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.024436 restraints weight = 97246.484| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 3.86 r_work: 0.2408 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15136 Z= 0.097 Angle : 0.575 10.328 20540 Z= 0.271 Chirality : 0.042 0.136 2283 Planarity : 0.004 0.049 2626 Dihedral : 5.369 41.796 2112 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.32 % Allowed : 4.94 % Favored : 94.75 % 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: 1.67 (0.21), residues: 1852 helix: 1.76 (0.19), residues: 794 sheet: -0.19 (0.32), residues: 295 loop : 1.19 (0.26), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 183 TYR 0.008 0.001 TYR E 188 PHE 0.006 0.001 PHE D 375 TRP 0.010 0.002 TRP E 79 HIS 0.002 0.000 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00213 (15135) covalent geometry : angle 0.57512 (20540) hydrogen bonds : bond 0.03029 ( 708) hydrogen bonds : angle 4.64280 ( 1842) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.504 Fit side-chains REVERT: C 82 MET cc_start: 0.9334 (tpp) cc_final: 0.8855 (tmm) REVERT: C 269 MET cc_start: 0.9014 (tpp) cc_final: 0.8804 (ttm) REVERT: C 355 MET cc_start: 0.9623 (mmm) cc_final: 0.9286 (mmp) REVERT: A 82 MET cc_start: 0.9670 (tpt) cc_final: 0.9160 (tpp) REVERT: A 227 MET cc_start: 0.8866 (mmm) cc_final: 0.8570 (tpt) REVERT: A 269 MET cc_start: 0.8950 (tpp) cc_final: 0.8597 (mtt) REVERT: A 313 MET cc_start: 0.9819 (tpp) cc_final: 0.9309 (tpp) REVERT: A 375 PHE cc_start: 0.7533 (m-80) cc_final: 0.7260 (m-80) REVERT: E 47 MET cc_start: 0.7028 (ppp) cc_final: 0.6388 (ppp) REVERT: E 355 MET cc_start: 0.9521 (mmp) cc_final: 0.9301 (mmm) REVERT: B 44 MET cc_start: 0.1032 (ptt) cc_final: 0.0595 (ptp) REVERT: B 227 MET cc_start: 0.9539 (tpt) cc_final: 0.9237 (mmm) REVERT: B 269 MET cc_start: 0.9308 (tpp) cc_final: 0.8864 (mtp) REVERT: B 305 MET cc_start: 0.9561 (mmm) cc_final: 0.9359 (mmm) REVERT: B 355 MET cc_start: 0.9588 (mmm) cc_final: 0.8891 (mpp) REVERT: D 269 MET cc_start: 0.9457 (tpp) cc_final: 0.9078 (mtp) outliers start: 5 outliers final: 3 residues processed: 91 average time/residue: 0.0831 time to fit residues: 12.4317 Evaluate side-chains 89 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain D residue 71 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 162 optimal weight: 6.9990 chunk 104 optimal weight: 0.0370 chunk 3 optimal weight: 0.0470 chunk 167 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.2846 r_free = 0.2846 target = 0.030117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.024551 restraints weight = 99499.791| |-----------------------------------------------------------------------------| r_work (start): 0.2582 rms_B_bonded: 3.71 r_work: 0.2440 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15136 Z= 0.134 Angle : 0.589 12.195 20540 Z= 0.275 Chirality : 0.042 0.134 2283 Planarity : 0.004 0.050 2626 Dihedral : 5.295 45.867 2112 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.44 % Allowed : 5.32 % Favored : 94.24 % 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: 1.50 (0.21), residues: 1852 helix: 1.63 (0.19), residues: 824 sheet: -0.29 (0.31), residues: 305 loop : 1.08 (0.27), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 95 TYR 0.010 0.001 TYR C 143 PHE 0.010 0.001 PHE B 375 TRP 0.010 0.001 TRP C 79 HIS 0.002 0.000 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00301 (15135) covalent geometry : angle 0.58902 (20540) hydrogen bonds : bond 0.03001 ( 708) hydrogen bonds : angle 4.63524 ( 1842) Misc. bond : bond 0.00067 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.390 Fit side-chains REVERT: C 82 MET cc_start: 0.9329 (tpp) cc_final: 0.9000 (tpt) REVERT: C 355 MET cc_start: 0.9648 (mmm) cc_final: 0.9295 (mmp) REVERT: A 82 MET cc_start: 0.9663 (tpt) cc_final: 0.9124 (tpp) REVERT: A 269 MET cc_start: 0.9001 (tpp) cc_final: 0.8680 (mtt) REVERT: A 305 MET cc_start: 0.9258 (mmt) cc_final: 0.8819 (mmm) REVERT: A 313 MET cc_start: 0.9785 (tpp) cc_final: 0.9318 (tpp) REVERT: A 375 PHE cc_start: 0.7566 (m-80) cc_final: 0.7265 (m-80) REVERT: E 47 MET cc_start: 0.6952 (ppp) cc_final: 0.6407 (ppp) REVERT: B 44 MET cc_start: 0.0968 (ptt) cc_final: 0.0646 (ptp) REVERT: B 227 MET cc_start: 0.9529 (tpt) cc_final: 0.9286 (tpt) REVERT: B 269 MET cc_start: 0.9272 (tpp) cc_final: 0.8848 (mtp) REVERT: B 305 MET cc_start: 0.9538 (mmm) cc_final: 0.9334 (mmm) REVERT: B 313 MET cc_start: 0.9765 (tpp) cc_final: 0.9238 (mmm) REVERT: B 355 MET cc_start: 0.9588 (mmm) cc_final: 0.9247 (mmp) REVERT: D 269 MET cc_start: 0.9430 (tpp) cc_final: 0.9049 (mtp) outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 0.0763 time to fit residues: 11.5187 Evaluate side-chains 93 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain D residue 71 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.2806 r_free = 0.2806 target = 0.029198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.023613 restraints weight = 100592.840| |-----------------------------------------------------------------------------| r_work (start): 0.2538 rms_B_bonded: 3.67 r_work: 0.2398 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15136 Z= 0.258 Angle : 0.672 12.941 20540 Z= 0.316 Chirality : 0.044 0.136 2283 Planarity : 0.004 0.047 2626 Dihedral : 5.596 47.066 2112 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.51 % Allowed : 5.70 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.21), residues: 1852 helix: 1.74 (0.19), residues: 799 sheet: -0.38 (0.31), residues: 305 loop : 1.17 (0.26), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 183 TYR 0.014 0.001 TYR A 143 PHE 0.013 0.001 PHE E 124 TRP 0.014 0.002 TRP C 79 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00564 (15135) covalent geometry : angle 0.67239 (20540) hydrogen bonds : bond 0.03360 ( 708) hydrogen bonds : angle 4.85027 ( 1842) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.582 Fit side-chains REVERT: C 82 MET cc_start: 0.9329 (tpp) cc_final: 0.8858 (tmm) REVERT: C 355 MET cc_start: 0.9636 (mmm) cc_final: 0.9314 (mmm) REVERT: A 82 MET cc_start: 0.9649 (tpt) cc_final: 0.9104 (tpp) REVERT: A 269 MET cc_start: 0.9006 (tpp) cc_final: 0.8660 (mtt) REVERT: A 313 MET cc_start: 0.9785 (tpp) cc_final: 0.9319 (tpp) REVERT: A 375 PHE cc_start: 0.7674 (m-80) cc_final: 0.7368 (m-80) REVERT: E 47 MET cc_start: 0.6982 (ppp) cc_final: 0.6368 (ppp) REVERT: E 132 MET cc_start: 0.9185 (tmm) cc_final: 0.8967 (tmm) REVERT: E 355 MET cc_start: 0.9533 (mmp) cc_final: 0.9233 (mmm) REVERT: B 44 MET cc_start: 0.0792 (ptt) cc_final: 0.0255 (ptp) REVERT: B 123 MET cc_start: 0.9689 (mmt) cc_final: 0.9474 (mmp) REVERT: B 132 MET cc_start: 0.9265 (tmm) cc_final: 0.9063 (tmm) REVERT: B 227 MET cc_start: 0.9532 (tpt) cc_final: 0.9278 (tpt) REVERT: B 269 MET cc_start: 0.9327 (tpp) cc_final: 0.8879 (mtp) REVERT: B 305 MET cc_start: 0.9527 (mmm) cc_final: 0.9307 (mmm) REVERT: B 313 MET cc_start: 0.9766 (tpp) cc_final: 0.9249 (mmm) REVERT: B 355 MET cc_start: 0.9598 (mmm) cc_final: 0.9273 (mmp) REVERT: D 269 MET cc_start: 0.9467 (tpp) cc_final: 0.9024 (mtp) outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.0841 time to fit residues: 13.0518 Evaluate side-chains 92 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain B residue 71 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 145 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.2795 r_free = 0.2795 target = 0.029335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.023548 restraints weight = 98501.587| |-----------------------------------------------------------------------------| r_work (start): 0.2517 rms_B_bonded: 3.92 r_work: 0.2369 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15136 Z= 0.171 Angle : 0.640 12.586 20540 Z= 0.295 Chirality : 0.042 0.134 2283 Planarity : 0.004 0.048 2626 Dihedral : 5.462 47.349 2112 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.25 % Allowed : 5.95 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.21), residues: 1852 helix: 1.77 (0.19), residues: 799 sheet: -0.35 (0.31), residues: 305 loop : 1.13 (0.26), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 183 TYR 0.018 0.001 TYR A 143 PHE 0.010 0.001 PHE E 124 TRP 0.013 0.002 TRP E 79 HIS 0.002 0.000 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00380 (15135) covalent geometry : angle 0.64008 (20540) hydrogen bonds : bond 0.03173 ( 708) hydrogen bonds : angle 4.70340 ( 1842) Misc. bond : bond 0.00074 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.579 Fit side-chains REVERT: C 82 MET cc_start: 0.9303 (tpp) cc_final: 0.8966 (tpt) REVERT: C 355 MET cc_start: 0.9655 (mmm) cc_final: 0.9280 (mmp) REVERT: A 82 MET cc_start: 0.9672 (tpt) cc_final: 0.9135 (tpp) REVERT: A 269 MET cc_start: 0.9015 (tpp) cc_final: 0.8660 (mtt) REVERT: A 299 MET cc_start: 0.8981 (ttm) cc_final: 0.8303 (ttp) REVERT: A 305 MET cc_start: 0.9226 (mmt) cc_final: 0.8873 (mmm) REVERT: A 313 MET cc_start: 0.9798 (tpp) cc_final: 0.9334 (tpp) REVERT: A 375 PHE cc_start: 0.7564 (m-80) cc_final: 0.7268 (m-80) REVERT: E 47 MET cc_start: 0.6939 (ppp) cc_final: 0.6420 (ppp) REVERT: E 132 MET cc_start: 0.9181 (tmm) cc_final: 0.8965 (tmm) REVERT: E 355 MET cc_start: 0.9528 (mmp) cc_final: 0.9255 (mmm) REVERT: B 44 MET cc_start: 0.0678 (ptt) cc_final: 0.0214 (ptp) REVERT: B 132 MET cc_start: 0.9270 (tmm) cc_final: 0.9051 (tmm) REVERT: B 227 MET cc_start: 0.9522 (tpt) cc_final: 0.9214 (mmm) REVERT: B 269 MET cc_start: 0.9316 (tpp) cc_final: 0.8857 (mtp) REVERT: B 305 MET cc_start: 0.9542 (mmm) cc_final: 0.9328 (mmm) REVERT: B 313 MET cc_start: 0.9755 (tpp) cc_final: 0.9115 (mmm) REVERT: B 355 MET cc_start: 0.9601 (mmm) cc_final: 0.9273 (mmp) REVERT: D 269 MET cc_start: 0.9430 (tpp) cc_final: 0.8983 (mtp) outliers start: 4 outliers final: 4 residues processed: 91 average time/residue: 0.0770 time to fit residues: 11.6036 Evaluate side-chains 91 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain B residue 71 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 121 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.2788 r_free = 0.2788 target = 0.029165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.023365 restraints weight = 98430.178| |-----------------------------------------------------------------------------| r_work (start): 0.2508 rms_B_bonded: 3.92 r_work: 0.2358 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15136 Z= 0.213 Angle : 0.650 12.646 20540 Z= 0.303 Chirality : 0.043 0.133 2283 Planarity : 0.004 0.047 2626 Dihedral : 5.541 49.501 2112 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.32 % Allowed : 5.89 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.21), residues: 1852 helix: 1.77 (0.19), residues: 799 sheet: -0.35 (0.31), residues: 305 loop : 1.12 (0.26), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 183 TYR 0.014 0.001 TYR A 143 PHE 0.008 0.001 PHE E 124 TRP 0.014 0.002 TRP E 79 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00469 (15135) covalent geometry : angle 0.64997 (20540) hydrogen bonds : bond 0.03251 ( 708) hydrogen bonds : angle 4.76288 ( 1842) Misc. bond : bond 0.00077 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2024.94 seconds wall clock time: 35 minutes 56.34 seconds (2156.34 seconds total)