Starting phenix.real_space_refine on Fri May 16 20:16:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gob_51496/05_2025/9gob_51496.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gob_51496/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gob_51496/05_2025/9gob_51496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gob_51496/05_2025/9gob_51496.map" model { file = "/net/cci-nas-00/data/ceres_data/9gob_51496/05_2025/9gob_51496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gob_51496/05_2025/9gob_51496.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.065 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.44, per 1000 atoms: 0.64 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: 3.97 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 2.18 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: 5.49 Time building geometry restraints manager: 4.57 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.650 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (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 TRP 0.025 0.004 TRP E 86 HIS 0.003 0.001 HIS D 101 PHE 0.008 0.001 PHE E 127 TYR 0.016 0.004 TYR D 188 ARG 0.028 0.005 ARG B 183 Details of bonding type rmsd hydrogen bonds : bond 0.14462 ( 708) hydrogen bonds : angle 7.46758 ( 1842) covalent geometry : bond 0.00307 (15135) covalent geometry : angle 0.73248 (20540) 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 : 1.744 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: 0.3209 time to fit residues: 54.2160 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 : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 75 optimal weight: 0.4980 chunk 146 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 162 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.030822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.025364 restraints weight = 98102.866| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 3.64 r_work: 0.2479 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15136 Z= 0.161 Angle : 0.642 7.475 20540 Z= 0.321 Chirality : 0.044 0.155 2283 Planarity : 0.004 0.050 2626 Dihedral : 6.824 69.680 2112 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1852 helix: 0.06 (0.18), residues: 824 sheet: -0.59 (0.29), residues: 305 loop : 0.71 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 340 HIS 0.002 0.001 HIS B 161 PHE 0.017 0.001 PHE E 375 TYR 0.011 0.001 TYR C 143 ARG 0.006 0.001 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 708) hydrogen bonds : angle 5.60725 ( 1842) covalent geometry : bond 0.00362 (15135) covalent geometry : angle 0.64228 (20540) Misc. bond : bond 0.00017 ( 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 92 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 227 MET cc_start: 0.9369 (tpt) cc_final: 0.8987 (tpt) REVERT: C 269 MET cc_start: 0.9085 (tpp) cc_final: 0.8736 (ttm) REVERT: C 355 MET cc_start: 0.9572 (mmm) cc_final: 0.9320 (mmp) REVERT: A 10 CYS cc_start: 0.8746 (t) cc_final: 0.8340 (t) REVERT: A 44 MET cc_start: 0.0124 (pmm) cc_final: -0.0746 (ptp) REVERT: A 82 MET cc_start: 0.9430 (tpp) cc_final: 0.9205 (tpt) REVERT: A 227 MET cc_start: 0.9320 (tpt) cc_final: 0.9066 (tpt) REVERT: A 269 MET cc_start: 0.8925 (tpp) cc_final: 0.8463 (mtt) REVERT: A 355 MET cc_start: 0.9376 (mmp) cc_final: 0.9145 (mmp) REVERT: E 119 MET cc_start: 0.9606 (mtm) cc_final: 0.9326 (mtp) REVERT: E 123 MET cc_start: 0.9627 (mmm) cc_final: 0.9414 (mmp) REVERT: E 132 MET cc_start: 0.9072 (tmm) cc_final: 0.8868 (tmm) REVERT: E 305 MET cc_start: 0.9444 (mmm) cc_final: 0.9175 (mmm) REVERT: E 313 MET cc_start: 0.9541 (tpp) cc_final: 0.9093 (tpt) REVERT: E 355 MET cc_start: 0.9492 (mmp) cc_final: 0.9178 (mmm) REVERT: B 82 MET cc_start: 0.9421 (tpp) cc_final: 0.9041 (tpt) REVERT: B 227 MET cc_start: 0.9542 (tpt) cc_final: 0.9037 (tpp) REVERT: B 313 MET cc_start: 0.9757 (tpp) cc_final: 0.9285 (mmm) REVERT: B 355 MET cc_start: 0.9557 (mmm) cc_final: 0.9251 (mmp) REVERT: D 132 MET cc_start: 0.9020 (tmm) cc_final: 0.8747 (tmm) REVERT: D 227 MET cc_start: 0.9165 (mmm) cc_final: 0.8901 (mmm) REVERT: D 269 MET cc_start: 0.9490 (tpp) cc_final: 0.8966 (mtp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2465 time to fit residues: 36.2595 Evaluate side-chains 88 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 73 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 9 optimal weight: 0.1980 chunk 173 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 overall best weight: 6.0388 ------------------------------------------------------------------------------- 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** A 173 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.028922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.023467 restraints weight = 100925.645| |-----------------------------------------------------------------------------| r_work (start): 0.2524 rms_B_bonded: 3.62 r_work: 0.2384 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 15136 Z= 0.339 Angle : 0.702 7.547 20540 Z= 0.349 Chirality : 0.046 0.150 2283 Planarity : 0.005 0.046 2626 Dihedral : 6.468 64.292 2112 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.13 % Allowed : 4.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1852 helix: 0.84 (0.18), residues: 819 sheet: -0.64 (0.30), residues: 325 loop : 0.97 (0.26), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 79 HIS 0.003 0.001 HIS E 371 PHE 0.012 0.001 PHE B 262 TYR 0.010 0.001 TYR B 294 ARG 0.005 0.001 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 708) hydrogen bonds : angle 5.49583 ( 1842) covalent geometry : bond 0.00739 (15135) covalent geometry : angle 0.70161 (20540) Misc. bond : bond 0.00145 ( 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: 2 poor density : 87 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 82 MET cc_start: 0.9316 (tpp) cc_final: 0.9104 (tpt) REVERT: C 269 MET cc_start: 0.9241 (tpp) cc_final: 0.8937 (ttm) REVERT: C 305 MET cc_start: 0.9490 (mmm) cc_final: 0.9262 (mmm) REVERT: C 355 MET cc_start: 0.9604 (mmm) cc_final: 0.9328 (mmp) REVERT: A 10 CYS cc_start: 0.8692 (t) cc_final: 0.8310 (t) REVERT: A 44 MET cc_start: -0.2055 (pmm) cc_final: -0.2303 (ptp) REVERT: A 82 MET cc_start: 0.9462 (tpp) cc_final: 0.9176 (tpp) REVERT: A 269 MET cc_start: 0.8959 (tpp) cc_final: 0.8562 (mtt) REVERT: E 119 MET cc_start: 0.9601 (mtm) cc_final: 0.9330 (mtp) REVERT: E 305 MET cc_start: 0.9525 (mmm) cc_final: 0.9281 (mmm) REVERT: E 313 MET cc_start: 0.9550 (tpp) cc_final: 0.9076 (tpt) REVERT: B 132 MET cc_start: 0.9406 (tmm) cc_final: 0.9201 (tmm) REVERT: B 305 MET cc_start: 0.9552 (mmm) cc_final: 0.9323 (mmm) REVERT: B 313 MET cc_start: 0.9770 (tpp) cc_final: 0.9152 (mmm) REVERT: B 355 MET cc_start: 0.9600 (mmm) cc_final: 0.9314 (mmp) REVERT: D 269 MET cc_start: 0.9518 (tpp) cc_final: 0.9030 (mtp) outliers start: 2 outliers final: 1 residues processed: 88 average time/residue: 0.2478 time to fit residues: 34.7515 Evaluate side-chains 87 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 160 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 149 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.9100 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.030420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.024808 restraints weight = 97012.057| |-----------------------------------------------------------------------------| r_work (start): 0.2580 rms_B_bonded: 3.79 r_work: 0.2434 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15136 Z= 0.100 Angle : 0.558 9.218 20540 Z= 0.272 Chirality : 0.042 0.135 2283 Planarity : 0.004 0.050 2626 Dihedral : 5.552 41.826 2112 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.19 % Allowed : 4.24 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.21), residues: 1852 helix: 1.27 (0.19), residues: 824 sheet: -0.21 (0.32), residues: 295 loop : 0.86 (0.26), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.002 0.001 HIS B 275 PHE 0.010 0.001 PHE E 375 TYR 0.010 0.001 TYR C 143 ARG 0.003 0.000 ARG D 95 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 708) hydrogen bonds : angle 4.85992 ( 1842) covalent geometry : bond 0.00219 (15135) covalent geometry : angle 0.55831 (20540) Misc. bond : bond 0.00073 ( 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 91 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 1.617 Fit side-chains REVERT: C 82 MET cc_start: 0.9342 (tpp) cc_final: 0.9023 (tpt) REVERT: C 269 MET cc_start: 0.8984 (tpp) cc_final: 0.8617 (ttm) REVERT: C 305 MET cc_start: 0.9447 (mmm) cc_final: 0.9202 (mmm) REVERT: C 355 MET cc_start: 0.9587 (mmm) cc_final: 0.9303 (mmp) REVERT: A 269 MET cc_start: 0.8894 (tpp) cc_final: 0.8500 (mtt) REVERT: A 283 MET cc_start: 0.9527 (mmm) cc_final: 0.9309 (mmm) REVERT: A 313 MET cc_start: 0.9814 (tpp) cc_final: 0.9340 (tpp) REVERT: E 305 MET cc_start: 0.9498 (mmm) cc_final: 0.9180 (mmm) REVERT: E 313 MET cc_start: 0.9522 (tpp) cc_final: 0.9054 (tpt) REVERT: E 355 MET cc_start: 0.9515 (mmp) cc_final: 0.9217 (mmm) REVERT: B 269 MET cc_start: 0.9277 (tpp) cc_final: 0.8911 (mtp) REVERT: B 305 MET cc_start: 0.9555 (mmm) cc_final: 0.9342 (mmm) REVERT: B 313 MET cc_start: 0.9756 (tpp) cc_final: 0.9240 (mmm) REVERT: B 355 MET cc_start: 0.9585 (mmm) cc_final: 0.9281 (mmp) REVERT: D 269 MET cc_start: 0.9425 (tpp) cc_final: 0.9053 (mtp) outliers start: 3 outliers final: 1 residues processed: 91 average time/residue: 0.2391 time to fit residues: 34.4603 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 : 1.558 ------------------------------------------------------------------------------- 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 172 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 32 optimal weight: 0.0980 chunk 78 optimal weight: 0.8980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.2834 r_free = 0.2834 target = 0.030141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.024547 restraints weight = 98663.615| |-----------------------------------------------------------------------------| r_work (start): 0.2570 rms_B_bonded: 3.83 r_work: 0.2424 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15136 Z= 0.117 Angle : 0.566 13.283 20540 Z= 0.269 Chirality : 0.042 0.172 2283 Planarity : 0.004 0.050 2626 Dihedral : 5.345 38.120 2112 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.25 % Allowed : 4.68 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.21), residues: 1852 helix: 1.39 (0.19), residues: 824 sheet: -0.19 (0.32), residues: 295 loop : 0.95 (0.26), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.002 0.000 HIS B 275 PHE 0.006 0.001 PHE D 124 TYR 0.010 0.001 TYR C 143 ARG 0.003 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03000 ( 708) hydrogen bonds : angle 4.74420 ( 1842) covalent geometry : bond 0.00261 (15135) covalent geometry : angle 0.56574 (20540) Misc. bond : bond 0.00074 ( 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 88 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 1.942 Fit side-chains REVERT: C 82 MET cc_start: 0.9357 (tpp) cc_final: 0.9037 (tpt) REVERT: C 132 MET cc_start: 0.9349 (tmm) cc_final: 0.9099 (tmm) REVERT: C 305 MET cc_start: 0.9433 (mmm) cc_final: 0.9208 (mmm) REVERT: C 355 MET cc_start: 0.9580 (mmm) cc_final: 0.9290 (mmp) REVERT: A 82 MET cc_start: 0.9641 (tpt) cc_final: 0.9209 (tpp) REVERT: A 269 MET cc_start: 0.8901 (tpp) cc_final: 0.8529 (mtt) REVERT: A 375 PHE cc_start: 0.6869 (m-80) cc_final: 0.6384 (m-80) REVERT: E 47 MET cc_start: 0.6899 (ppp) cc_final: 0.6469 (ppp) REVERT: E 305 MET cc_start: 0.9504 (mmm) cc_final: 0.9256 (mmm) REVERT: E 313 MET cc_start: 0.9548 (tpp) cc_final: 0.9085 (tpt) REVERT: E 355 MET cc_start: 0.9496 (mmp) cc_final: 0.9245 (mmm) REVERT: E 375 PHE cc_start: 0.7170 (t80) cc_final: 0.6926 (t80) REVERT: B 44 MET cc_start: 0.0327 (ptt) cc_final: -0.0156 (ptp) REVERT: B 132 MET cc_start: 0.9412 (tmm) cc_final: 0.9068 (tmm) REVERT: B 269 MET cc_start: 0.9283 (tpp) cc_final: 0.8818 (mtp) REVERT: B 305 MET cc_start: 0.9531 (mmm) cc_final: 0.9319 (mmm) REVERT: B 355 MET cc_start: 0.9584 (mmm) cc_final: 0.9260 (mmp) REVERT: D 269 MET cc_start: 0.9439 (tpp) cc_final: 0.9047 (mtp) outliers start: 4 outliers final: 2 residues processed: 88 average time/residue: 0.2589 time to fit residues: 37.5291 Evaluate side-chains 86 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain B residue 71 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 32 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 143 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS 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 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 = 0.2791 r_free = 0.2791 target = 0.028910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.023308 restraints weight = 101012.801| |-----------------------------------------------------------------------------| r_work (start): 0.2521 rms_B_bonded: 3.71 r_work: 0.2379 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 15136 Z= 0.314 Angle : 0.681 11.095 20540 Z= 0.329 Chirality : 0.045 0.144 2283 Planarity : 0.004 0.048 2626 Dihedral : 5.794 43.660 2112 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.38 % Allowed : 4.75 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.21), residues: 1852 helix: 1.42 (0.19), residues: 824 sheet: -0.56 (0.29), residues: 325 loop : 1.04 (0.27), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 79 HIS 0.003 0.001 HIS A 275 PHE 0.010 0.001 PHE C 21 TYR 0.009 0.001 TYR C 143 ARG 0.003 0.000 ARG C 183 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 708) hydrogen bonds : angle 5.06308 ( 1842) covalent geometry : bond 0.00683 (15135) covalent geometry : angle 0.68076 (20540) Misc. bond : bond 0.00089 ( 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 91 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 1.645 Fit side-chains REVERT: C 82 MET cc_start: 0.9360 (tpp) cc_final: 0.8892 (tmm) REVERT: C 132 MET cc_start: 0.9411 (tmm) cc_final: 0.9115 (tmm) REVERT: C 355 MET cc_start: 0.9620 (mmm) cc_final: 0.9329 (mmm) REVERT: A 82 MET cc_start: 0.9645 (tpt) cc_final: 0.9098 (tpp) REVERT: A 269 MET cc_start: 0.9042 (tpp) cc_final: 0.8691 (mtt) REVERT: A 299 MET cc_start: 0.9000 (ttm) cc_final: 0.8322 (ttp) REVERT: A 313 MET cc_start: 0.9782 (tpp) cc_final: 0.9262 (tpp) REVERT: A 375 PHE cc_start: 0.7336 (m-80) cc_final: 0.6754 (m-80) REVERT: E 47 MET cc_start: 0.6976 (ppp) cc_final: 0.6458 (ppp) REVERT: E 82 MET cc_start: 0.9693 (tpt) cc_final: 0.9443 (tpt) REVERT: E 132 MET cc_start: 0.9224 (tmm) cc_final: 0.8981 (tmm) REVERT: E 305 MET cc_start: 0.9501 (mmm) cc_final: 0.9224 (mmm) REVERT: E 313 MET cc_start: 0.9552 (tpp) cc_final: 0.9085 (tpt) REVERT: E 375 PHE cc_start: 0.7123 (t80) cc_final: 0.6680 (t80) REVERT: B 44 MET cc_start: 0.0816 (ptt) cc_final: 0.0271 (ptp) REVERT: B 123 MET cc_start: 0.9701 (mmt) cc_final: 0.9435 (mmp) REVERT: B 269 MET cc_start: 0.9308 (tpp) cc_final: 0.8837 (mtp) REVERT: B 305 MET cc_start: 0.9538 (mmm) cc_final: 0.9298 (mmm) REVERT: B 355 MET cc_start: 0.9582 (mmm) cc_final: 0.9272 (mmp) REVERT: D 269 MET cc_start: 0.9508 (tpp) cc_final: 0.9038 (mtp) outliers start: 6 outliers final: 3 residues processed: 90 average time/residue: 0.2863 time to fit residues: 42.2397 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 : 1.599 ------------------------------------------------------------------------------- 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 176 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 176 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.2836 r_free = 0.2836 target = 0.029919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.024441 restraints weight = 99883.883| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 3.66 r_work: 0.2436 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15136 Z= 0.142 Angle : 0.594 11.804 20540 Z= 0.280 Chirality : 0.042 0.134 2283 Planarity : 0.004 0.049 2626 Dihedral : 5.477 41.587 2112 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.44 % Allowed : 4.94 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.21), residues: 1852 helix: 1.68 (0.19), residues: 799 sheet: -0.31 (0.31), residues: 305 loop : 1.12 (0.26), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 79 HIS 0.002 0.000 HIS B 275 PHE 0.006 0.001 PHE C 262 TYR 0.009 0.001 TYR A 143 ARG 0.002 0.000 ARG C 183 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 708) hydrogen bonds : angle 4.73978 ( 1842) covalent geometry : bond 0.00317 (15135) covalent geometry : angle 0.59438 (20540) Misc. bond : bond 0.00074 ( 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: 7 poor density : 85 time to evaluate : 1.643 Fit side-chains REVERT: C 82 MET cc_start: 0.9346 (tpp) cc_final: 0.8863 (tmm) REVERT: C 132 MET cc_start: 0.9390 (tmm) cc_final: 0.9127 (tmm) REVERT: C 355 MET cc_start: 0.9630 (mmm) cc_final: 0.9328 (mmp) REVERT: A 82 MET cc_start: 0.9661 (tpt) cc_final: 0.9025 (tpp) REVERT: A 269 MET cc_start: 0.8982 (tpp) cc_final: 0.8638 (mtt) REVERT: A 299 MET cc_start: 0.9021 (ttm) cc_final: 0.8385 (ttt) REVERT: A 313 MET cc_start: 0.9776 (tpp) cc_final: 0.9301 (tpp) REVERT: A 375 PHE cc_start: 0.7066 (m-80) cc_final: 0.6464 (m-80) REVERT: E 47 MET cc_start: 0.6826 (ppp) cc_final: 0.6415 (ppp) REVERT: E 305 MET cc_start: 0.9481 (mmm) cc_final: 0.9209 (mmm) REVERT: E 355 MET cc_start: 0.9535 (mmp) cc_final: 0.9288 (mmm) REVERT: B 44 MET cc_start: 0.1448 (ptt) cc_final: 0.0846 (ptp) REVERT: B 269 MET cc_start: 0.9253 (tpp) cc_final: 0.8814 (mtp) REVERT: B 305 MET cc_start: 0.9540 (mmm) cc_final: 0.9317 (mmm) REVERT: B 355 MET cc_start: 0.9600 (mmm) cc_final: 0.9278 (mmp) REVERT: D 269 MET cc_start: 0.9442 (tpp) cc_final: 0.9060 (mtp) outliers start: 7 outliers final: 4 residues processed: 91 average time/residue: 0.2220 time to fit residues: 32.9537 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 : 1.574 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.2817 r_free = 0.2817 target = 0.029401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.023830 restraints weight = 99948.476| |-----------------------------------------------------------------------------| r_work (start): 0.2543 rms_B_bonded: 3.69 r_work: 0.2402 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15136 Z= 0.230 Angle : 0.648 10.598 20540 Z= 0.306 Chirality : 0.043 0.137 2283 Planarity : 0.004 0.047 2626 Dihedral : 5.610 46.013 2112 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.32 % Allowed : 5.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.21), residues: 1852 helix: 1.55 (0.19), residues: 824 sheet: -0.39 (0.30), residues: 315 loop : 0.97 (0.27), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.002 0.001 HIS A 275 PHE 0.009 0.001 PHE E 375 TYR 0.010 0.001 TYR A 143 ARG 0.003 0.000 ARG C 183 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 708) hydrogen bonds : angle 4.84677 ( 1842) covalent geometry : bond 0.00505 (15135) covalent geometry : angle 0.64786 (20540) Misc. bond : bond 0.00079 ( 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 91 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 1.794 Fit side-chains REVERT: C 82 MET cc_start: 0.9357 (tpp) cc_final: 0.8923 (tmm) REVERT: C 355 MET cc_start: 0.9613 (mmm) cc_final: 0.9273 (mmp) REVERT: A 82 MET cc_start: 0.9647 (tpt) cc_final: 0.9107 (tpp) REVERT: A 269 MET cc_start: 0.9022 (tpp) cc_final: 0.8691 (mtt) REVERT: A 283 MET cc_start: 0.9483 (mmm) cc_final: 0.9257 (mmm) REVERT: A 305 MET cc_start: 0.9301 (mmt) cc_final: 0.8885 (mmm) REVERT: A 375 PHE cc_start: 0.7161 (m-80) cc_final: 0.6572 (m-80) REVERT: E 47 MET cc_start: 0.6913 (ppp) cc_final: 0.6447 (ppp) REVERT: E 132 MET cc_start: 0.9209 (tmm) cc_final: 0.8980 (tmm) REVERT: E 305 MET cc_start: 0.9491 (mmm) cc_final: 0.9212 (mmm) REVERT: E 355 MET cc_start: 0.9535 (mmp) cc_final: 0.9272 (mmm) REVERT: E 375 PHE cc_start: 0.7130 (t80) cc_final: 0.6649 (t80) REVERT: B 44 MET cc_start: 0.1179 (ptt) cc_final: 0.0524 (ptp) REVERT: B 269 MET cc_start: 0.9320 (tpp) cc_final: 0.8875 (mtp) REVERT: B 305 MET cc_start: 0.9525 (mmm) cc_final: 0.9293 (mmm) REVERT: B 355 MET cc_start: 0.9605 (mmm) cc_final: 0.9284 (mmp) REVERT: D 269 MET cc_start: 0.9496 (tpp) cc_final: 0.9067 (mtp) outliers start: 5 outliers final: 4 residues processed: 90 average time/residue: 0.2591 time to fit residues: 37.8921 Evaluate side-chains 90 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 93 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 175 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 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** ** 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 = 0.2822 r_free = 0.2822 target = 0.029506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.023962 restraints weight = 99249.398| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 3.66 r_work: 0.2409 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15136 Z= 0.210 Angle : 0.642 11.476 20540 Z= 0.301 Chirality : 0.043 0.134 2283 Planarity : 0.004 0.048 2626 Dihedral : 5.591 47.744 2112 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.44 % Allowed : 5.38 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.21), residues: 1852 helix: 1.70 (0.19), residues: 799 sheet: -0.35 (0.31), residues: 305 loop : 1.10 (0.26), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.002 0.001 HIS B 275 PHE 0.009 0.001 PHE E 375 TYR 0.013 0.001 TYR A 143 ARG 0.003 0.000 ARG C 183 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 708) hydrogen bonds : angle 4.80178 ( 1842) covalent geometry : bond 0.00464 (15135) covalent geometry : angle 0.64209 (20540) 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 93 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: C 82 MET cc_start: 0.9368 (tpp) cc_final: 0.8942 (tmm) REVERT: C 355 MET cc_start: 0.9627 (mmm) cc_final: 0.9284 (mmp) REVERT: A 82 MET cc_start: 0.9651 (tpt) cc_final: 0.9102 (tpp) REVERT: A 269 MET cc_start: 0.8995 (tpp) cc_final: 0.8664 (mtt) REVERT: A 283 MET cc_start: 0.9489 (mmm) cc_final: 0.9253 (mmm) REVERT: A 305 MET cc_start: 0.9339 (mmt) cc_final: 0.8929 (mmm) REVERT: E 47 MET cc_start: 0.6926 (ppp) cc_final: 0.6531 (ppp) REVERT: E 132 MET cc_start: 0.9217 (tmm) cc_final: 0.8984 (tmm) REVERT: E 305 MET cc_start: 0.9488 (mmm) cc_final: 0.9215 (mmm) REVERT: E 355 MET cc_start: 0.9539 (mmp) cc_final: 0.9279 (mmm) REVERT: E 375 PHE cc_start: 0.7108 (t80) cc_final: 0.6641 (t80) REVERT: B 44 MET cc_start: 0.1614 (ptt) cc_final: 0.0885 (ptp) REVERT: B 227 MET cc_start: 0.9713 (mmp) cc_final: 0.9233 (mmm) REVERT: B 269 MET cc_start: 0.9287 (tpp) cc_final: 0.8867 (mtp) REVERT: B 305 MET cc_start: 0.9539 (mmm) cc_final: 0.9301 (mmm) REVERT: B 355 MET cc_start: 0.9598 (mmm) cc_final: 0.9273 (mmp) REVERT: D 269 MET cc_start: 0.9478 (tpp) cc_final: 0.9083 (mtp) outliers start: 7 outliers final: 7 residues processed: 92 average time/residue: 0.2239 time to fit residues: 33.4143 Evaluate side-chains 93 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 334 GLU 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 176 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 139 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 147 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.2838 r_free = 0.2838 target = 0.030096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.024542 restraints weight = 98358.907| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 3.81 r_work: 0.2426 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15136 Z= 0.102 Angle : 0.602 13.029 20540 Z= 0.277 Chirality : 0.041 0.136 2283 Planarity : 0.004 0.050 2626 Dihedral : 5.222 47.611 2112 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.38 % Allowed : 5.51 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.21), residues: 1852 helix: 1.67 (0.19), residues: 824 sheet: -0.18 (0.32), residues: 295 loop : 1.28 (0.27), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 86 HIS 0.002 0.000 HIS B 275 PHE 0.020 0.001 PHE A 375 TYR 0.013 0.001 TYR A 143 ARG 0.003 0.000 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.02920 ( 708) hydrogen bonds : angle 4.54995 ( 1842) covalent geometry : bond 0.00229 (15135) covalent geometry : angle 0.60170 (20540) Misc. bond : bond 0.00059 ( 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 94 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 1.690 Fit side-chains revert: symmetry clash REVERT: C 82 MET cc_start: 0.9357 (tpp) cc_final: 0.8933 (tmm) REVERT: C 355 MET cc_start: 0.9630 (mmm) cc_final: 0.9281 (mmp) REVERT: A 82 MET cc_start: 0.9699 (tpt) cc_final: 0.9162 (tpp) REVERT: A 269 MET cc_start: 0.9023 (tpp) cc_final: 0.8712 (mtt) REVERT: A 313 MET cc_start: 0.9762 (tpp) cc_final: 0.9494 (tpp) REVERT: E 47 MET cc_start: 0.6770 (ppp) cc_final: 0.6428 (ppp) REVERT: E 132 MET cc_start: 0.9214 (tmm) cc_final: 0.8974 (tmm) REVERT: E 283 MET cc_start: 0.9411 (mmm) cc_final: 0.9177 (mmm) REVERT: E 305 MET cc_start: 0.9485 (mmm) cc_final: 0.9215 (mmm) REVERT: E 355 MET cc_start: 0.9523 (mmp) cc_final: 0.9286 (mmm) REVERT: E 375 PHE cc_start: 0.7079 (t80) cc_final: 0.6841 (t80) REVERT: B 44 MET cc_start: 0.1658 (ptt) cc_final: 0.0641 (ptp) REVERT: B 227 MET cc_start: 0.9745 (mmp) cc_final: 0.9256 (mmm) REVERT: B 269 MET cc_start: 0.9252 (tpp) cc_final: 0.8821 (mtp) REVERT: B 305 MET cc_start: 0.9544 (mmm) cc_final: 0.9336 (mmm) REVERT: B 313 MET cc_start: 0.9513 (mmm) cc_final: 0.8962 (tpp) REVERT: B 355 MET cc_start: 0.9587 (mmm) cc_final: 0.9275 (mmp) REVERT: D 269 MET cc_start: 0.9443 (tpp) cc_final: 0.9108 (mtp) outliers start: 6 outliers final: 6 residues processed: 94 average time/residue: 0.2363 time to fit residues: 36.0906 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 : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 334 GLU 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 39 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 165 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.2786 r_free = 0.2786 target = 0.029011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.023222 restraints weight = 100141.436| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 3.93 r_work: 0.2355 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15136 Z= 0.241 Angle : 0.659 12.830 20540 Z= 0.309 Chirality : 0.043 0.133 2283 Planarity : 0.004 0.048 2626 Dihedral : 5.484 49.996 2112 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.38 % Allowed : 5.89 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.21), residues: 1852 helix: 1.57 (0.19), residues: 829 sheet: -0.36 (0.31), residues: 305 loop : 0.94 (0.27), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.002 0.001 HIS A 275 PHE 0.009 0.001 PHE E 375 TYR 0.013 0.001 TYR A 143 ARG 0.002 0.000 ARG C 290 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 708) hydrogen bonds : angle 4.78608 ( 1842) covalent geometry : bond 0.00527 (15135) covalent geometry : angle 0.65901 (20540) Misc. bond : bond 0.00077 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5319.77 seconds wall clock time: 93 minutes 46.80 seconds (5626.80 seconds total)