Starting phenix.real_space_refine on Wed Jul 30 03:22:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kll_0711/07_2025/6kll_0711.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kll_0711/07_2025/6kll_0711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kll_0711/07_2025/6kll_0711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kll_0711/07_2025/6kll_0711.map" model { file = "/net/cci-nas-00/data/ceres_data/6kll_0711/07_2025/6kll_0711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kll_0711/07_2025/6kll_0711.cif" } resolution = 3.0 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= 0.003 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 8 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1980 2.21 5 O 2264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11748 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 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} Restraints were copied for chains: C, B, D Time building chain proxies: 6.03, per 1000 atoms: 0.51 Number of scatterers: 11748 At special positions: 0 Unit cell: (87.74, 96.3, 165.85, 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 84 16.00 P 8 15.00 Mg 4 11.99 O 2264 8.00 N 1980 7.00 C 7408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.8 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 20 sheets defined 49.5% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.563A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.502A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.119A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 146 removed outlier: 3.630A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.592A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.662A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.528A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.781A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.640A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.552A pdb=" N GLY A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 removed outlier: 6.345A pdb=" N THR A 351 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.890A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 372 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.563A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.502A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.119A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 3.630A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.593A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.662A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.527A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.782A pdb=" N TYR B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 319 removed outlier: 3.639A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.552A pdb=" N GLY B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 removed outlier: 6.345A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.889A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 372 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.563A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.501A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.120A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 146 removed outlier: 3.630A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.592A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.661A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.527A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.782A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 319 removed outlier: 3.640A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 removed outlier: 3.552A pdb=" N GLY C 342 " --> pdb=" O SER C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 353 removed outlier: 6.345A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.890A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 372 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.563A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.503A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.119A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 removed outlier: 3.629A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.592A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.662A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.527A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.782A pdb=" N TYR D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 319 removed outlier: 3.639A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 removed outlier: 3.552A pdb=" N GLY D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 353 removed outlier: 6.345A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.889A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 372 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.066A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.615A pdb=" N SER A 155 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.065A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.616A pdb=" N SER B 155 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.066A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.615A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.066A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.615A pdb=" N SER D 155 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 496 hydrogen bonds defined for protein. 1224 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: 4.34 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3832 1.34 - 1.46: 2526 1.46 - 1.58: 5482 1.58 - 1.69: 16 1.69 - 1.81: 148 Bond restraints: 12004 Sorted by residual: bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.04e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 6.94e+00 bond pdb=" CA LEU A 104 " pdb=" CB LEU A 104 " ideal model delta sigma weight residual 1.528 1.496 0.033 1.51e-02 4.39e+03 4.66e+00 ... (remaining 11999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15528 1.55 - 3.11: 625 3.11 - 4.66: 87 4.66 - 6.21: 44 6.21 - 7.76: 8 Bond angle restraints: 16292 Sorted by residual: angle pdb=" CB GLU C 4 " pdb=" CG GLU C 4 " pdb=" CD GLU C 4 " ideal model delta sigma weight residual 112.60 119.71 -7.11 1.70e+00 3.46e-01 1.75e+01 angle pdb=" CB GLU A 4 " pdb=" CG GLU A 4 " pdb=" CD GLU A 4 " ideal model delta sigma weight residual 112.60 119.71 -7.11 1.70e+00 3.46e-01 1.75e+01 angle pdb=" CB GLU D 4 " pdb=" CG GLU D 4 " pdb=" CD GLU D 4 " ideal model delta sigma weight residual 112.60 119.68 -7.08 1.70e+00 3.46e-01 1.73e+01 angle pdb=" CB GLU B 4 " pdb=" CG GLU B 4 " pdb=" CD GLU B 4 " ideal model delta sigma weight residual 112.60 119.66 -7.06 1.70e+00 3.46e-01 1.73e+01 angle pdb=" CA GLU D 4 " pdb=" CB GLU D 4 " pdb=" CG GLU D 4 " ideal model delta sigma weight residual 114.10 121.86 -7.76 2.00e+00 2.50e-01 1.51e+01 ... (remaining 16287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.69: 6531 20.69 - 41.39: 597 41.39 - 62.08: 80 62.08 - 82.77: 4 82.77 - 103.47: 8 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" C5' ADP B 802 " pdb=" O5' ADP B 802 " pdb=" PA ADP B 802 " pdb=" O2A ADP B 802 " ideal model delta sinusoidal sigma weight residual -60.00 43.47 -103.47 1 2.00e+01 2.50e-03 2.96e+01 dihedral pdb=" C5' ADP C 802 " pdb=" O5' ADP C 802 " pdb=" PA ADP C 802 " pdb=" O2A ADP C 802 " ideal model delta sinusoidal sigma weight residual -60.00 43.47 -103.46 1 2.00e+01 2.50e-03 2.96e+01 dihedral pdb=" C5' ADP A 802 " pdb=" O5' ADP A 802 " pdb=" PA ADP A 802 " pdb=" O2A ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 43.44 -103.43 1 2.00e+01 2.50e-03 2.96e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1008 0.042 - 0.084: 597 0.084 - 0.126: 183 0.126 - 0.168: 16 0.168 - 0.210: 4 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CB VAL C 370 " pdb=" CA VAL C 370 " pdb=" CG1 VAL C 370 " pdb=" CG2 VAL C 370 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB VAL D 370 " pdb=" CA VAL D 370 " pdb=" CG1 VAL D 370 " pdb=" CG2 VAL D 370 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB VAL A 370 " pdb=" CA VAL A 370 " pdb=" CG1 VAL A 370 " pdb=" CG2 VAL A 370 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO D 243 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO B 243 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO C 243 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " 0.021 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 92 2.53 - 3.13: 8712 3.13 - 3.72: 17521 3.72 - 4.31: 26814 4.31 - 4.90: 44339 Nonbonded interactions: 97478 Sorted by model distance: nonbonded pdb="MG MG A 801 " pdb=" O1B ADP A 802 " model vdw 1.944 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 1.944 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 1.944 2.170 nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 1.945 2.170 nonbonded pdb=" O GLY D 156 " pdb=" OG1 THR D 303 " model vdw 2.173 3.040 ... (remaining 97473 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.400 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.180 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 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 : 0.007 0.060 12004 Z= 0.324 Angle : 0.776 7.763 16292 Z= 0.445 Chirality : 0.052 0.210 1808 Planarity : 0.004 0.038 2084 Dihedral : 15.546 103.465 4468 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 7.64 % Allowed : 8.28 % Favored : 84.08 % 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: -3.74 (0.18), residues: 1468 helix: -3.54 (0.13), residues: 568 sheet: -1.95 (0.30), residues: 244 loop : -1.44 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 79 HIS 0.003 0.001 HIS B 275 PHE 0.011 0.002 PHE B 124 TYR 0.007 0.001 TYR C 69 ARG 0.003 0.001 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.24383 ( 496) hydrogen bonds : angle 8.75520 ( 1224) covalent geometry : bond 0.00717 (12004) covalent geometry : angle 0.77605 (16292) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 78 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.8314 (mmt) cc_final: 0.7231 (mmm) REVERT: B 82 MET cc_start: 0.8125 (tpt) cc_final: 0.7872 (tpt) REVERT: C 4 GLU cc_start: 0.5388 (OUTLIER) cc_final: 0.4140 (tm-30) REVERT: C 5 THR cc_start: 0.6181 (OUTLIER) cc_final: 0.5470 (m) REVERT: C 123 MET cc_start: 0.8647 (mmm) cc_final: 0.8398 (mmt) REVERT: C 233 SER cc_start: 0.5856 (OUTLIER) cc_final: 0.5385 (t) REVERT: D 4 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.4748 (tm-30) outliers start: 96 outliers final: 18 residues processed: 167 average time/residue: 1.1663 time to fit residues: 213.6132 Evaluate side-chains 89 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 277 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 161 HIS B 59 GLN B 161 HIS C 161 HIS D 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.044996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.037009 restraints weight = 48165.567| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.26 r_work: 0.2594 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12004 Z= 0.154 Angle : 0.636 5.759 16292 Z= 0.322 Chirality : 0.047 0.145 1808 Planarity : 0.004 0.032 2084 Dihedral : 8.481 95.733 1702 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.03 % Allowed : 13.69 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.20), residues: 1468 helix: -2.04 (0.19), residues: 532 sheet: -1.47 (0.29), residues: 280 loop : -0.65 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.005 0.001 HIS D 101 PHE 0.011 0.001 PHE C 223 TYR 0.009 0.001 TYR D 294 ARG 0.006 0.000 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 496) hydrogen bonds : angle 5.36270 ( 1224) covalent geometry : bond 0.00347 (12004) covalent geometry : angle 0.63600 (16292) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 68 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9387 (mtp) cc_final: 0.8903 (tpp) REVERT: B 44 MET cc_start: 0.8577 (mmt) cc_final: 0.8176 (mmm) REVERT: B 82 MET cc_start: 0.9006 (tpt) cc_final: 0.8557 (tpt) REVERT: B 325 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7763 (ptt) REVERT: C 50 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7787 (mmtm) REVERT: C 82 MET cc_start: 0.9227 (mmm) cc_final: 0.9015 (tpt) REVERT: C 233 SER cc_start: 0.5882 (OUTLIER) cc_final: 0.5582 (t) REVERT: D 82 MET cc_start: 0.9177 (tpt) cc_final: 0.8874 (tpt) REVERT: D 325 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7899 (ptp) outliers start: 38 outliers final: 12 residues processed: 98 average time/residue: 1.3526 time to fit residues: 144.0524 Evaluate side-chains 82 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 44 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 101 HIS B 59 GLN C 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.043765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.035780 restraints weight = 49133.062| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 3.30 r_work: 0.2550 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12004 Z= 0.199 Angle : 0.615 5.772 16292 Z= 0.305 Chirality : 0.048 0.135 1808 Planarity : 0.004 0.036 2084 Dihedral : 7.583 89.918 1684 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.23 % Allowed : 15.53 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1468 helix: -1.24 (0.20), residues: 584 sheet: -0.95 (0.31), residues: 276 loop : -0.21 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.005 0.001 HIS D 275 PHE 0.013 0.001 PHE C 223 TYR 0.010 0.001 TYR A 133 ARG 0.005 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 496) hydrogen bonds : angle 4.89951 ( 1224) covalent geometry : bond 0.00456 (12004) covalent geometry : angle 0.61501 (16292) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: A 305 MET cc_start: 0.9385 (mtp) cc_final: 0.9123 (tpp) REVERT: B 44 MET cc_start: 0.8528 (mmt) cc_final: 0.8267 (mmm) REVERT: B 123 MET cc_start: 0.9414 (mmt) cc_final: 0.9211 (mmt) REVERT: B 227 MET cc_start: 0.8952 (tpt) cc_final: 0.8752 (mmm) REVERT: C 50 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7813 (mmtm) REVERT: D 82 MET cc_start: 0.9248 (tpt) cc_final: 0.9033 (tpt) outliers start: 28 outliers final: 6 residues processed: 87 average time/residue: 1.3613 time to fit residues: 128.7357 Evaluate side-chains 73 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 34 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 54 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.044486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.036514 restraints weight = 47991.773| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.24 r_work: 0.2578 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12004 Z= 0.116 Angle : 0.552 5.643 16292 Z= 0.268 Chirality : 0.045 0.130 1808 Planarity : 0.003 0.027 2084 Dihedral : 6.917 85.319 1674 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.27 % Allowed : 17.60 % Favored : 81.13 % 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: -0.80 (0.22), residues: 1468 helix: -0.70 (0.21), residues: 584 sheet: -0.76 (0.32), residues: 276 loop : 0.06 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 340 HIS 0.004 0.001 HIS D 275 PHE 0.008 0.001 PHE C 255 TYR 0.006 0.001 TYR C 69 ARG 0.003 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.02754 ( 496) hydrogen bonds : angle 4.72212 ( 1224) covalent geometry : bond 0.00262 (12004) covalent geometry : angle 0.55232 (16292) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.8582 (mmt) cc_final: 0.6334 (mpp) REVERT: C 50 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7822 (mmtm) REVERT: C 82 MET cc_start: 0.9221 (mmm) cc_final: 0.8921 (mmm) outliers start: 16 outliers final: 7 residues processed: 77 average time/residue: 1.4668 time to fit residues: 122.2338 Evaluate side-chains 74 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain D residue 89 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 110 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 59 GLN B 12 ASN B 101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.042183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.034275 restraints weight = 49087.645| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 3.21 r_work: 0.2500 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 12004 Z= 0.320 Angle : 0.668 7.140 16292 Z= 0.329 Chirality : 0.051 0.150 1808 Planarity : 0.004 0.032 2084 Dihedral : 7.033 88.474 1673 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.91 % Allowed : 16.96 % Favored : 81.13 % 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: -0.55 (0.22), residues: 1468 helix: -0.53 (0.21), residues: 564 sheet: -0.67 (0.32), residues: 280 loop : 0.23 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 79 HIS 0.004 0.001 HIS A 40 PHE 0.016 0.002 PHE C 223 TYR 0.009 0.001 TYR A 166 ARG 0.003 0.001 ARG C 254 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 496) hydrogen bonds : angle 4.82484 ( 1224) covalent geometry : bond 0.00729 (12004) covalent geometry : angle 0.66774 (16292) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.8693 (mmt) cc_final: 0.6487 (mpp) REVERT: B 123 MET cc_start: 0.9488 (mmt) cc_final: 0.9273 (mmt) REVERT: C 50 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7912 (mmtm) REVERT: D 270 GLU cc_start: 0.5901 (OUTLIER) cc_final: 0.3883 (mp0) REVERT: D 325 MET cc_start: 0.8416 (ptp) cc_final: 0.8107 (ptp) outliers start: 24 outliers final: 12 residues processed: 83 average time/residue: 1.4283 time to fit residues: 128.7997 Evaluate side-chains 80 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 270 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 137 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN C 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.043984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.035974 restraints weight = 48482.009| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 3.31 r_work: 0.2553 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12004 Z= 0.104 Angle : 0.544 5.815 16292 Z= 0.262 Chirality : 0.045 0.133 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.742 82.883 1673 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.80 % Allowed : 18.23 % Favored : 80.97 % 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: 0.04 (0.23), residues: 1468 helix: 0.05 (0.23), residues: 548 sheet: -0.56 (0.32), residues: 280 loop : 0.56 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 356 HIS 0.004 0.001 HIS D 275 PHE 0.009 0.001 PHE C 255 TYR 0.007 0.001 TYR D 69 ARG 0.003 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.02642 ( 496) hydrogen bonds : angle 4.62002 ( 1224) covalent geometry : bond 0.00234 (12004) covalent geometry : angle 0.54443 (16292) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.8643 (mmt) cc_final: 0.6441 (mpp) REVERT: B 227 MET cc_start: 0.9013 (mmm) cc_final: 0.8641 (mmm) REVERT: C 50 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7853 (mmtm) REVERT: C 233 SER cc_start: 0.6226 (OUTLIER) cc_final: 0.6021 (t) REVERT: D 325 MET cc_start: 0.8351 (ptp) cc_final: 0.8049 (ptp) outliers start: 10 outliers final: 3 residues processed: 73 average time/residue: 1.5765 time to fit residues: 124.2406 Evaluate side-chains 71 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain D residue 89 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 0.0970 chunk 123 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.043970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.035959 restraints weight = 48884.075| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.33 r_work: 0.2553 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12004 Z= 0.121 Angle : 0.537 5.967 16292 Z= 0.256 Chirality : 0.045 0.133 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.461 77.741 1673 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.96 % Allowed : 18.71 % Favored : 80.33 % 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: 0.17 (0.23), residues: 1468 helix: 0.23 (0.23), residues: 572 sheet: -0.52 (0.32), residues: 280 loop : 0.60 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 356 HIS 0.003 0.001 HIS D 275 PHE 0.009 0.001 PHE C 255 TYR 0.007 0.001 TYR D 69 ARG 0.003 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.02627 ( 496) hydrogen bonds : angle 4.52132 ( 1224) covalent geometry : bond 0.00277 (12004) covalent geometry : angle 0.53656 (16292) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: A 305 MET cc_start: 0.9308 (mtp) cc_final: 0.8926 (tpp) REVERT: B 44 MET cc_start: 0.8624 (mmt) cc_final: 0.6477 (mpp) REVERT: B 227 MET cc_start: 0.8911 (mmm) cc_final: 0.8635 (mmm) REVERT: D 270 GLU cc_start: 0.5772 (OUTLIER) cc_final: 0.3841 (mp0) REVERT: D 325 MET cc_start: 0.8356 (ptp) cc_final: 0.8075 (ptp) outliers start: 12 outliers final: 4 residues processed: 76 average time/residue: 1.5324 time to fit residues: 125.7635 Evaluate side-chains 71 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain D residue 270 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 73 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 76 optimal weight: 0.0370 chunk 116 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.044559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.036526 restraints weight = 48524.142| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.34 r_work: 0.2581 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12004 Z= 0.089 Angle : 0.517 5.851 16292 Z= 0.246 Chirality : 0.044 0.130 1808 Planarity : 0.003 0.029 2084 Dihedral : 6.222 73.750 1672 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.56 % Allowed : 18.87 % Favored : 80.57 % 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: 0.61 (0.23), residues: 1468 helix: 0.64 (0.23), residues: 548 sheet: -0.21 (0.31), residues: 304 loop : 0.78 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 356 HIS 0.003 0.001 HIS D 275 PHE 0.009 0.001 PHE C 255 TYR 0.008 0.001 TYR A 279 ARG 0.002 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.02407 ( 496) hydrogen bonds : angle 4.46614 ( 1224) covalent geometry : bond 0.00201 (12004) covalent geometry : angle 0.51675 (16292) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: A 283 MET cc_start: 0.8802 (tpp) cc_final: 0.8496 (mpp) REVERT: A 305 MET cc_start: 0.9237 (mtp) cc_final: 0.8899 (tpp) REVERT: B 44 MET cc_start: 0.8519 (mmt) cc_final: 0.6380 (mpp) REVERT: B 227 MET cc_start: 0.8922 (mmm) cc_final: 0.8507 (mmm) REVERT: C 82 MET cc_start: 0.9162 (tpt) cc_final: 0.8773 (mmm) REVERT: D 325 MET cc_start: 0.8336 (ptp) cc_final: 0.8059 (ptp) outliers start: 7 outliers final: 4 residues processed: 73 average time/residue: 1.5249 time to fit residues: 120.1425 Evaluate side-chains 70 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 21 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 0.0470 chunk 30 optimal weight: 0.9980 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.045298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.037243 restraints weight = 48408.368| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.40 r_work: 0.2594 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12004 Z= 0.086 Angle : 0.517 9.750 16292 Z= 0.242 Chirality : 0.044 0.128 1808 Planarity : 0.003 0.031 2084 Dihedral : 5.939 68.336 1672 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.40 % Allowed : 19.03 % Favored : 80.57 % 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: 1.05 (0.24), residues: 1468 helix: 0.94 (0.24), residues: 544 sheet: -0.02 (0.31), residues: 296 loop : 1.12 (0.29), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 356 HIS 0.004 0.001 HIS D 275 PHE 0.009 0.001 PHE C 255 TYR 0.006 0.001 TYR D 69 ARG 0.004 0.000 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.02292 ( 496) hydrogen bonds : angle 4.38721 ( 1224) covalent geometry : bond 0.00194 (12004) covalent geometry : angle 0.51661 (16292) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 1.293 Fit side-chains REVERT: A 283 MET cc_start: 0.8813 (tpp) cc_final: 0.8433 (mpp) REVERT: A 305 MET cc_start: 0.9176 (mtp) cc_final: 0.8918 (tpp) REVERT: B 44 MET cc_start: 0.8474 (mmt) cc_final: 0.6264 (mpp) REVERT: B 227 MET cc_start: 0.8896 (mmm) cc_final: 0.8522 (mmm) REVERT: C 82 MET cc_start: 0.9108 (tpt) cc_final: 0.8686 (mmm) REVERT: D 325 MET cc_start: 0.8290 (ptp) cc_final: 0.8038 (ptp) outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 1.4999 time to fit residues: 113.3758 Evaluate side-chains 68 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 0.4980 chunk 147 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 105 optimal weight: 0.0870 chunk 121 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 15 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.045893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.037832 restraints weight = 47820.385| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.40 r_work: 0.2617 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12004 Z= 0.078 Angle : 0.520 11.084 16292 Z= 0.242 Chirality : 0.044 0.128 1808 Planarity : 0.003 0.033 2084 Dihedral : 5.706 62.814 1672 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.32 % Allowed : 19.19 % Favored : 80.49 % 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 (0.24), residues: 1468 helix: 1.14 (0.24), residues: 544 sheet: 0.03 (0.31), residues: 296 loop : 1.21 (0.29), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 356 HIS 0.004 0.001 HIS B 275 PHE 0.008 0.001 PHE C 255 TYR 0.006 0.001 TYR A 279 ARG 0.003 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.02185 ( 496) hydrogen bonds : angle 4.34602 ( 1224) covalent geometry : bond 0.00173 (12004) covalent geometry : angle 0.51975 (16292) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: A 283 MET cc_start: 0.8789 (tpp) cc_final: 0.8442 (mpp) REVERT: B 44 MET cc_start: 0.8436 (mmt) cc_final: 0.6244 (mpp) REVERT: B 227 MET cc_start: 0.8890 (mmm) cc_final: 0.8509 (mmm) REVERT: B 269 MET cc_start: 0.9116 (mtp) cc_final: 0.8793 (ttm) REVERT: B 283 MET cc_start: 0.9062 (tpp) cc_final: 0.8818 (tpp) REVERT: C 82 MET cc_start: 0.9060 (tpt) cc_final: 0.8323 (mmm) REVERT: D 325 MET cc_start: 0.8259 (ptp) cc_final: 0.8018 (ptp) outliers start: 4 outliers final: 3 residues processed: 70 average time/residue: 1.5157 time to fit residues: 114.6239 Evaluate side-chains 69 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 143 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.042418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.034529 restraints weight = 49275.814| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 3.24 r_work: 0.2495 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.039 12004 Z= 0.335 Angle : 0.670 9.297 16292 Z= 0.326 Chirality : 0.051 0.148 1808 Planarity : 0.004 0.030 2084 Dihedral : 6.371 75.868 1672 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.48 % Allowed : 18.87 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1468 helix: 0.35 (0.22), residues: 572 sheet: -0.46 (0.32), residues: 280 loop : 0.58 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 79 HIS 0.004 0.001 HIS A 40 PHE 0.013 0.002 PHE C 223 TYR 0.013 0.001 TYR A 166 ARG 0.004 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 496) hydrogen bonds : angle 4.62977 ( 1224) covalent geometry : bond 0.00761 (12004) covalent geometry : angle 0.66956 (16292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5541.35 seconds wall clock time: 95 minutes 58.00 seconds (5758.00 seconds total)