Starting phenix.real_space_refine on Fri Sep 11 22:10:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kll_0711/09_2026/6kll_0711.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kll_0711/09_2026/6kll_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6kll_0711/09_2026/6kll_0711.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kll_0711/09_2026/6kll_0711.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kll_0711/09_2026/6kll_0711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kll_0711/09_2026/6kll_0711.map" model { file = "/net/cci-nas-00/data/ceres_data/6kll_0711/09_2026/6kll_0711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kll_0711/09_2026/6kll_0711.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: B, C, D Time building chain proxies: 2.74, per 1000 atoms: 0.23 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: 0.87 Conformation dependent library (CDL) restraints added in 585.8 milliseconds 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: 0.46 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: 2.15 Time building geometry restraints manager: 1.23 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 1.370 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.001 ARG B 177 TYR 0.007 0.001 TYR C 69 PHE 0.011 0.002 PHE B 124 TRP 0.011 0.002 TRP C 79 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.32 (12004) covalent geometry : angle 0.77605 / 0.44 (16292) hydrogen bonds : bond 0.24383 / 16.35 ( 496) hydrogen bonds : angle 8.75520 / 6.05 ( 1224) *********************** 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 : 0.502 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: 0.5855 (OUTLIER) cc_final: 0.5385 (t) REVERT: D 4 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.4748 (tm-30) outliers start: 96 outliers final: 18 residues processed: 167 average time/residue: 0.5491 time to fit residues: 100.3858 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 : 0.477 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 161 HIS B 59 GLN D 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.045927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.037790 restraints weight = 48250.602| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.34 r_work: 0.2612 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12004 Z= 0.122 Angle : 0.619 5.642 16292 Z= 0.312 Chirality : 0.046 0.141 1808 Planarity : 0.004 0.031 2084 Dihedral : 8.413 94.022 1702 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.79 % Allowed : 13.30 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.20), residues: 1468 helix: -2.13 (0.18), residues: 556 sheet: -1.24 (0.30), residues: 260 loop : -0.66 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 372 TYR 0.009 0.001 TYR D 294 PHE 0.009 0.001 PHE C 223 TRP 0.009 0.001 TRP B 340 HIS 0.005 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (12004) covalent geometry : angle 0.61851 / 0.31 (16292) hydrogen bonds : bond 0.03712 / 2.48 ( 496) hydrogen bonds : angle 5.37560 / 3.80 ( 1224) *********************** 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: 35 poor density : 71 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9354 (mtp) cc_final: 0.8873 (tpp) REVERT: B 44 MET cc_start: 0.8540 (mmt) cc_final: 0.8107 (mmm) REVERT: B 82 MET cc_start: 0.8973 (tpt) cc_final: 0.8521 (tpt) REVERT: B 325 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7702 (ptt) REVERT: C 50 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7756 (mmtm) REVERT: C 82 MET cc_start: 0.9196 (mmm) cc_final: 0.8979 (tpt) REVERT: C 233 SER cc_start: 0.5820 (OUTLIER) cc_final: 0.5524 (t) REVERT: D 82 MET cc_start: 0.9150 (tpt) cc_final: 0.8815 (tpt) REVERT: D 325 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7885 (ptp) outliers start: 35 outliers final: 10 residues processed: 97 average time/residue: 0.6603 time to fit residues: 69.2784 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 : 0.493 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 98 optimal weight: 0.4980 chunk 76 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 59 GLN A 101 HIS B 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.035195 restraints weight = 49627.057| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 3.30 r_work: 0.2529 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 12004 Z= 0.258 Angle : 0.654 5.978 16292 Z= 0.326 Chirality : 0.049 0.144 1808 Planarity : 0.004 0.030 2084 Dihedral : 7.687 91.814 1684 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.15 % Allowed : 15.37 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.21), residues: 1468 helix: -1.41 (0.20), residues: 584 sheet: -1.03 (0.32), residues: 276 loop : -0.29 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 372 TYR 0.010 0.001 TYR A 133 PHE 0.015 0.002 PHE C 223 TRP 0.009 0.002 TRP C 79 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.26 (12004) covalent geometry : angle 0.65438 / 0.33 (16292) hydrogen bonds : bond 0.03873 / 2.59 ( 496) hydrogen bonds : angle 4.97662 / 3.52 ( 1224) *********************** 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 94 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 305 MET cc_start: 0.9413 (mtp) cc_final: 0.8959 (tpp) REVERT: B 44 MET cc_start: 0.8492 (mmt) cc_final: 0.8252 (mmm) REVERT: C 50 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7839 (mmtm) REVERT: C 325 MET cc_start: 0.8543 (ptp) cc_final: 0.8329 (ptp) REVERT: D 82 MET cc_start: 0.9295 (tpt) cc_final: 0.9083 (tpt) REVERT: D 270 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.3847 (mp0) outliers start: 27 outliers final: 8 residues processed: 88 average time/residue: 0.6527 time to fit residues: 62.0592 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 : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain B residue 89 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 10 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.044530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.036525 restraints weight = 48751.224| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.28 r_work: 0.2575 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2369 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= 0.106 Angle : 0.553 5.592 16292 Z= 0.268 Chirality : 0.045 0.135 1808 Planarity : 0.003 0.027 2084 Dihedral : 6.938 85.438 1675 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.19 % Allowed : 17.60 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.22), residues: 1468 helix: -0.66 (0.22), residues: 560 sheet: -0.78 (0.31), residues: 280 loop : 0.15 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 372 TYR 0.006 0.001 TYR C 69 PHE 0.009 0.001 PHE C 255 TRP 0.007 0.001 TRP C 356 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (12004) covalent geometry : angle 0.55280 / 0.27 (16292) hydrogen bonds : bond 0.02707 / 1.79 ( 496) hydrogen bonds : angle 4.74594 / 3.37 ( 1224) *********************** 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 82 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 305 MET cc_start: 0.9395 (mtp) cc_final: 0.9145 (tpp) REVERT: B 44 MET cc_start: 0.8647 (mmt) cc_final: 0.6410 (mpp) REVERT: B 227 MET cc_start: 0.8954 (mmm) cc_final: 0.8620 (mmm) REVERT: C 50 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7812 (mmtm) REVERT: C 325 MET cc_start: 0.8324 (ptp) cc_final: 0.8120 (ptp) outliers start: 15 outliers final: 6 residues processed: 76 average time/residue: 0.7279 time to fit residues: 59.6743 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 : 0.531 ------------------------------------------------------------------------------- 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 82 MET Chi-restraints excluded: chain B residue 323 SER 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 72 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 144 optimal weight: 0.0170 chunk 93 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 overall best weight: 6.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.042137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.034203 restraints weight = 49738.497| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 3.29 r_work: 0.2501 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 12004 Z= 0.300 Angle : 0.646 6.247 16292 Z= 0.319 Chirality : 0.050 0.147 1808 Planarity : 0.004 0.032 2084 Dihedral : 6.967 87.027 1673 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.43 % Allowed : 17.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.22), residues: 1468 helix: -0.54 (0.22), residues: 564 sheet: -0.70 (0.32), residues: 280 loop : 0.25 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 254 TYR 0.010 0.001 TYR C 188 PHE 0.015 0.002 PHE C 223 TRP 0.010 0.001 TRP C 79 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.30 (12004) covalent geometry : angle 0.64619 / 0.32 (16292) hydrogen bonds : bond 0.03562 / 2.38 ( 496) hydrogen bonds : angle 4.80545 / 3.41 ( 1224) *********************** 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 84 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 305 MET cc_start: 0.9402 (mtp) cc_final: 0.8878 (tpp) REVERT: B 44 MET cc_start: 0.8603 (mmt) cc_final: 0.6356 (mpp) REVERT: C 50 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7862 (mmtm) REVERT: D 270 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.3977 (mp0) outliers start: 18 outliers final: 11 residues processed: 80 average time/residue: 0.6976 time to fit residues: 60.2689 Evaluate side-chains 79 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 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 112 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 HIS C 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.043686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.035746 restraints weight = 48862.951| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 3.29 r_work: 0.2556 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12004 Z= 0.109 Angle : 0.546 5.734 16292 Z= 0.262 Chirality : 0.045 0.133 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.741 83.109 1673 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.80 % Allowed : 18.47 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.23), residues: 1468 helix: -0.09 (0.22), residues: 564 sheet: -0.58 (0.32), residues: 280 loop : 0.44 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 372 TYR 0.006 0.001 TYR D 69 PHE 0.009 0.001 PHE C 255 TRP 0.008 0.001 TRP A 340 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (12004) covalent geometry : angle 0.54550 / 0.26 (16292) hydrogen bonds : bond 0.02729 / 1.81 ( 496) hydrogen bonds : angle 4.63674 / 3.30 ( 1224) *********************** 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 : 0.438 Fit side-chains revert: symmetry clash REVERT: A 305 MET cc_start: 0.9368 (mtp) cc_final: 0.9131 (tpp) REVERT: B 44 MET cc_start: 0.8549 (mmt) cc_final: 0.6419 (mpp) REVERT: C 50 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7862 (mmtm) REVERT: C 82 MET cc_start: 0.9240 (tpt) cc_final: 0.8555 (mmm) REVERT: D 270 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.3916 (mp0) outliers start: 10 outliers final: 3 residues processed: 72 average time/residue: 0.7296 time to fit residues: 56.4981 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 : 0.459 ------------------------------------------------------------------------------- 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 D residue 89 THR Chi-restraints excluded: chain D residue 270 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 121 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 41 optimal weight: 0.0030 chunk 62 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 overall best weight: 2.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.043564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.035650 restraints weight = 48987.245| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.26 r_work: 0.2557 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12004 Z= 0.135 Angle : 0.544 6.164 16292 Z= 0.261 Chirality : 0.046 0.131 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.491 79.520 1673 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.88 % Allowed : 19.19 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.23), residues: 1468 helix: 0.13 (0.22), residues: 572 sheet: -0.27 (0.31), residues: 304 loop : 0.56 (0.28), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 372 TYR 0.007 0.001 TYR D 69 PHE 0.009 0.001 PHE C 255 TRP 0.007 0.001 TRP A 340 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (12004) covalent geometry : angle 0.54411 / 0.26 (16292) hydrogen bonds : bond 0.02684 / 1.78 ( 496) hydrogen bonds : angle 4.54035 / 3.24 ( 1224) *********************** 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 77 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 305 MET cc_start: 0.9368 (mtp) cc_final: 0.9131 (tpp) REVERT: B 44 MET cc_start: 0.8597 (mmt) cc_final: 0.6369 (mpp) REVERT: B 227 MET cc_start: 0.8964 (mmm) cc_final: 0.8568 (mmm) REVERT: D 270 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.3902 (mp0) outliers start: 11 outliers final: 3 residues processed: 72 average time/residue: 0.6942 time to fit residues: 53.8814 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 : 0.478 ------------------------------------------------------------------------------- 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 270 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.043925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.035917 restraints weight = 48906.449| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 3.37 r_work: 0.2565 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2921 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= 0.113 Angle : 0.529 5.859 16292 Z= 0.252 Chirality : 0.045 0.128 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.312 76.283 1672 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.56 % Allowed : 19.59 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.23), residues: 1468 helix: 0.51 (0.23), residues: 548 sheet: -0.20 (0.31), residues: 304 loop : 0.72 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 372 TYR 0.007 0.001 TYR A 279 PHE 0.009 0.001 PHE C 255 TRP 0.007 0.001 TRP A 340 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (12004) covalent geometry : angle 0.52852 / 0.25 (16292) hydrogen bonds : bond 0.02559 / 1.69 ( 496) hydrogen bonds : angle 4.51177 / 3.22 ( 1224) *********************** 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 : 0.517 Fit side-chains revert: symmetry clash REVERT: A 283 MET cc_start: 0.8737 (tpp) cc_final: 0.8513 (mpp) REVERT: A 305 MET cc_start: 0.9350 (mtp) cc_final: 0.9107 (tpp) REVERT: B 44 MET cc_start: 0.8564 (mmt) cc_final: 0.6384 (mpp) REVERT: B 227 MET cc_start: 0.8899 (mmm) cc_final: 0.8517 (mmm) REVERT: C 82 MET cc_start: 0.9196 (tpt) cc_final: 0.8732 (mmm) REVERT: D 270 GLU cc_start: 0.5721 (OUTLIER) cc_final: 0.3902 (mp0) outliers start: 7 outliers final: 3 residues processed: 70 average time/residue: 0.7076 time to fit residues: 53.2504 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 : 0.395 ------------------------------------------------------------------------------- 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 270 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 132 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 0.0010 chunk 26 optimal weight: 0.0980 chunk 88 optimal weight: 0.0370 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.0268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 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 = 0.2984 r_free = 0.2984 target = 0.044806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.036805 restraints weight = 48328.431| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.37 r_work: 0.2587 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3049 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= 0.088 Angle : 0.513 5.867 16292 Z= 0.243 Chirality : 0.044 0.130 1808 Planarity : 0.003 0.030 2084 Dihedral : 6.040 70.618 1672 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.56 % Allowed : 19.35 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.24), residues: 1468 helix: 0.76 (0.23), residues: 548 sheet: 0.00 (0.31), residues: 296 loop : 1.04 (0.29), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 372 TYR 0.008 0.001 TYR A 279 PHE 0.009 0.001 PHE C 255 TRP 0.009 0.001 TRP C 356 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (12004) covalent geometry : angle 0.51334 / 0.24 (16292) hydrogen bonds : bond 0.02319 / 1.54 ( 496) hydrogen bonds : angle 4.44131 / 3.18 ( 1224) *********************** 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 73 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.504 Fit side-chains REVERT: A 283 MET cc_start: 0.8796 (tpp) cc_final: 0.8518 (mpp) REVERT: A 305 MET cc_start: 0.9335 (mtp) cc_final: 0.9104 (tpp) REVERT: B 44 MET cc_start: 0.8526 (mmt) cc_final: 0.6331 (mpp) REVERT: B 227 MET cc_start: 0.8911 (mmm) cc_final: 0.8532 (mmm) REVERT: C 82 MET cc_start: 0.9153 (tpt) cc_final: 0.8660 (mmm) REVERT: D 270 GLU cc_start: 0.5682 (OUTLIER) cc_final: 0.3839 (mp0) outliers start: 7 outliers final: 3 residues processed: 70 average time/residue: 0.7551 time to fit residues: 56.9874 Evaluate side-chains 69 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 65 optimal weight: 0.0980 chunk 51 optimal weight: 0.0670 chunk 103 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 147 optimal weight: 0.0980 chunk 102 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 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 = 0.2995 r_free = 0.2995 target = 0.045188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.037168 restraints weight = 48753.071| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.40 r_work: 0.2601 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12004 Z= 0.082 Angle : 0.519 8.343 16292 Z= 0.244 Chirality : 0.044 0.129 1808 Planarity : 0.003 0.030 2084 Dihedral : 5.850 66.224 1672 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.40 % Allowed : 19.67 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.24), residues: 1468 helix: 0.93 (0.24), residues: 548 sheet: 0.03 (0.31), residues: 296 loop : 1.13 (0.29), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 372 TYR 0.010 0.001 TYR B 279 PHE 0.008 0.001 PHE C 255 TRP 0.009 0.001 TRP C 356 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.08 (12004) covalent geometry : angle 0.51853 / 0.24 (16292) hydrogen bonds : bond 0.02284 / 1.51 ( 496) hydrogen bonds : angle 4.39733 / 3.14 ( 1224) ********************** 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 71 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 283 MET cc_start: 0.8788 (tpp) cc_final: 0.8513 (mpp) REVERT: A 305 MET cc_start: 0.9337 (mtp) cc_final: 0.9134 (tpp) REVERT: B 44 MET cc_start: 0.8566 (mmt) cc_final: 0.6302 (mpp) REVERT: B 227 MET cc_start: 0.8916 (mmm) cc_final: 0.8533 (mmm) REVERT: C 82 MET cc_start: 0.9142 (tpt) cc_final: 0.8640 (mmm) REVERT: D 270 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.3816 (mp0) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.7455 time to fit residues: 55.2851 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 : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 270 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 130 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 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 = 0.2984 r_free = 0.2984 target = 0.044511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.036604 restraints weight = 48418.360| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 3.19 r_work: 0.2596 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.3120 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= 0.126 Angle : 0.531 7.529 16292 Z= 0.250 Chirality : 0.045 0.130 1808 Planarity : 0.003 0.031 2084 Dihedral : 5.841 66.045 1672 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.40 % Allowed : 19.59 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.24), residues: 1468 helix: 0.95 (0.23), residues: 548 sheet: 0.04 (0.31), residues: 296 loop : 1.07 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 290 TYR 0.006 0.001 TYR A 279 PHE 0.009 0.001 PHE C 255 TRP 0.007 0.001 TRP D 79 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (12004) covalent geometry : angle 0.53100 / 0.25 (16292) hydrogen bonds : bond 0.02494 / 1.66 ( 496) hydrogen bonds : angle 4.38874 / 3.14 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.28 seconds wall clock time: 46 minutes 4.83 seconds (2764.83 seconds total)