Starting phenix.real_space_refine on Fri Jun 13 07:36:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f8p_28932/06_2025/8f8p_28932.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f8p_28932/06_2025/8f8p_28932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f8p_28932/06_2025/8f8p_28932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f8p_28932/06_2025/8f8p_28932.map" model { file = "/net/cci-nas-00/data/ceres_data/8f8p_28932/06_2025/8f8p_28932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f8p_28932/06_2025/8f8p_28932.cif" } resolution = 2.26 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= 0.003 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9235 2.51 5 N 2470 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14640 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "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, E, D Time building chain proxies: 6.57, per 1000 atoms: 0.45 Number of scatterers: 14640 At special positions: 0 Unit cell: (77.76, 99.36, 195.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2815 8.00 N 2470 7.00 C 9235 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: 3.68 Conformation dependent library (CDL) restraints added in 2.0 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 30 sheets defined 50.4% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.722A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.309A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.628A pdb=" N GLY A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.839A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.614A 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 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.237A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 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 348 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.598A pdb=" N CYS A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.722A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.309A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.628A pdb=" N GLY B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.839A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.614A 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 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.237A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 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 348 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.598A pdb=" N CYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.723A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.309A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.627A pdb=" N GLY C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.838A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.615A 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 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.236A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 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 348 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.598A pdb=" N CYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.723A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.308A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.627A pdb=" N GLY D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.838A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.614A 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 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.236A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 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 348 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.598A pdb=" N CYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.723A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.309A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.628A pdb=" N GLY E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.840A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.614A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.237A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.598A pdb=" N CYS E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.588A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (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: 6.505A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.549A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.505A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.632A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.506A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.775A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.506A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.588A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.506A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 724 hydrogen bonds defined for protein. 1863 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: 4.86 Time building geometry restraints manager: 4.31 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: 4717 1.34 - 1.46: 3198 1.46 - 1.58: 6845 1.58 - 1.70: 15 1.70 - 1.82: 185 Bond restraints: 14960 Sorted by residual: bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.36e+00 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 19753 2.10 - 4.20: 391 4.20 - 6.30: 134 6.30 - 8.40: 22 8.40 - 10.50: 5 Bond angle restraints: 20305 Sorted by residual: angle pdb=" C GLY C 46 " pdb=" N MET C 47 " pdb=" CA MET C 47 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C GLY B 46 " pdb=" N MET B 47 " pdb=" CA MET B 47 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C GLY E 46 " pdb=" N MET E 47 " pdb=" CA MET E 47 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C GLY D 46 " pdb=" N MET D 47 " pdb=" CA MET D 47 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C GLY A 46 " pdb=" N MET A 47 " pdb=" CA MET A 47 " ideal model delta sigma weight residual 121.54 129.38 -7.84 1.91e+00 2.74e-01 1.69e+01 ... (remaining 20300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 8610 35.73 - 71.46: 355 71.46 - 107.19: 20 107.19 - 142.92: 5 142.92 - 178.65: 5 Dihedral angle restraints: 8995 sinusoidal: 3635 harmonic: 5360 Sorted by residual: dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 121.35 178.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 121.36 178.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 121.37 178.63 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1287 0.033 - 0.065: 594 0.065 - 0.098: 214 0.098 - 0.131: 135 0.131 - 0.163: 25 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CA CYS E 257 " pdb=" N CYS E 257 " pdb=" C CYS E 257 " pdb=" CB CYS E 257 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CB ILE E 309 " pdb=" CA ILE E 309 " pdb=" CG1 ILE E 309 " pdb=" CG2 ILE E 309 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 2252 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO D 243 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO B 243 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO C 243 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " 0.027 5.00e-02 4.00e+02 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4212 2.82 - 3.34: 11721 3.34 - 3.86: 24582 3.86 - 4.38: 29091 4.38 - 4.90: 50352 Nonbonded interactions: 119958 Sorted by model distance: nonbonded pdb=" O GLN A 314 " pdb=" OG1 THR A 318 " model vdw 2.301 3.040 nonbonded pdb=" O GLN D 314 " pdb=" OG1 THR D 318 " model vdw 2.301 3.040 nonbonded pdb=" O GLN E 314 " pdb=" OG1 THR E 318 " model vdw 2.301 3.040 nonbonded pdb=" O GLN C 314 " pdb=" OG1 THR C 318 " model vdw 2.302 3.040 nonbonded pdb=" O GLN B 314 " pdb=" OG1 THR B 318 " model vdw 2.302 3.040 ... (remaining 119953 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' 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: 1.140 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 32.970 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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 : 0.004 0.055 14960 Z= 0.189 Angle : 0.825 10.502 20305 Z= 0.421 Chirality : 0.049 0.163 2255 Planarity : 0.006 0.049 2595 Dihedral : 17.731 178.653 5565 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.04 % Allowed : 22.81 % Favored : 75.14 % 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: -1.31 (0.19), residues: 1830 helix: -1.96 (0.14), residues: 745 sheet: 1.04 (0.30), residues: 345 loop : -0.37 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 356 HIS 0.003 0.001 HIS A 161 PHE 0.015 0.001 PHE B 255 TYR 0.010 0.001 TYR C 143 ARG 0.006 0.001 ARG E 206 Details of bonding type rmsd hydrogen bonds : bond 0.17660 ( 708) hydrogen bonds : angle 6.71820 ( 1863) covalent geometry : bond 0.00409 (14960) covalent geometry : angle 0.82549 (20305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 374 time to evaluate : 2.139 Fit side-chains revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8356 (m110) cc_final: 0.8152 (m-40) REVERT: A 115 ASN cc_start: 0.8126 (t0) cc_final: 0.7919 (t0) REVERT: A 252 ASN cc_start: 0.8441 (p0) cc_final: 0.8238 (p0) REVERT: B 225 ASN cc_start: 0.7838 (m-40) cc_final: 0.7575 (m-40) REVERT: B 283 MET cc_start: 0.8490 (mmm) cc_final: 0.8254 (mmt) REVERT: D 227 MET cc_start: 0.8628 (mmm) cc_final: 0.8342 (mmm) REVERT: D 288 ASP cc_start: 0.7881 (m-30) cc_final: 0.7665 (m-30) REVERT: D 299 MET cc_start: 0.8900 (mtm) cc_final: 0.8592 (mtm) outliers start: 32 outliers final: 11 residues processed: 391 average time/residue: 1.6382 time to fit residues: 690.3379 Evaluate side-chains 310 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 299 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 0.5980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 49 GLN A 59 GLN A 78 ASN A 162 ASN B 12 ASN B 59 GLN B 78 ASN B 115 ASN B 297 ASN D 78 ASN D 162 ASN D 297 ASN E 173 HIS E 280 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.107705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.099937 restraints weight = 19202.527| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.18 r_work: 0.3387 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14960 Z= 0.217 Angle : 0.650 7.273 20305 Z= 0.325 Chirality : 0.049 0.183 2255 Planarity : 0.005 0.038 2595 Dihedral : 9.570 156.772 2098 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.51 % Allowed : 19.23 % Favored : 77.25 % 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: -0.08 (0.20), residues: 1830 helix: -0.50 (0.18), residues: 770 sheet: 1.08 (0.29), residues: 340 loop : 0.14 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.008 0.002 HIS E 371 PHE 0.019 0.002 PHE B 127 TYR 0.015 0.001 TYR E 169 ARG 0.007 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 708) hydrogen bonds : angle 4.65476 ( 1863) covalent geometry : bond 0.00524 (14960) covalent geometry : angle 0.65012 (20305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 341 time to evaluate : 1.913 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.8389 (ttp) cc_final: 0.8170 (ptm) REVERT: A 176 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7928 (mtp) REVERT: B 47 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.5942 (ppp) REVERT: D 299 MET cc_start: 0.8901 (mtm) cc_final: 0.8659 (mtm) REVERT: E 78 ASN cc_start: 0.8269 (t0) cc_final: 0.8016 (t0) REVERT: E 107 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7741 (tt0) outliers start: 55 outliers final: 17 residues processed: 368 average time/residue: 1.7663 time to fit residues: 699.2138 Evaluate side-chains 323 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 303 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 180 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 297 ASN B 59 GLN B 78 ASN B 246 GLN B 297 ASN C 162 ASN C 246 GLN D 12 ASN D 115 ASN D 162 ASN D 297 ASN D 353 GLN E 297 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.108407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.100680 restraints weight = 19179.386| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.17 r_work: 0.3399 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14960 Z= 0.134 Angle : 0.565 6.577 20305 Z= 0.276 Chirality : 0.045 0.138 2255 Planarity : 0.004 0.039 2595 Dihedral : 6.884 104.253 2085 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.07 % Allowed : 20.45 % Favored : 76.49 % 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: 0.25 (0.20), residues: 1830 helix: 0.01 (0.18), residues: 800 sheet: 1.08 (0.29), residues: 340 loop : 0.11 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 79 HIS 0.004 0.001 HIS E 101 PHE 0.011 0.001 PHE B 127 TYR 0.007 0.001 TYR C 188 ARG 0.008 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 708) hydrogen bonds : angle 4.33339 ( 1863) covalent geometry : bond 0.00318 (14960) covalent geometry : angle 0.56522 (20305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 2.017 Fit side-chains REVERT: B 47 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.5901 (ppp) REVERT: D 132 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8100 (ttp) REVERT: D 299 MET cc_start: 0.8869 (mtm) cc_final: 0.8579 (mtm) REVERT: E 6 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7911 (t) REVERT: E 107 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: E 227 MET cc_start: 0.8872 (mmm) cc_final: 0.8654 (mmm) outliers start: 48 outliers final: 20 residues processed: 341 average time/residue: 1.9155 time to fit residues: 701.2540 Evaluate side-chains 320 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 296 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 336 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 49 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 162 ASN B 59 GLN B 246 GLN C 246 GLN C 263 GLN C 353 GLN D 115 ASN D 162 ASN D 297 ASN D 353 GLN E 12 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.105405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.097917 restraints weight = 18995.295| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.13 r_work: 0.3353 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 14960 Z= 0.343 Angle : 0.687 8.281 20305 Z= 0.342 Chirality : 0.054 0.210 2255 Planarity : 0.005 0.051 2595 Dihedral : 7.445 110.343 2085 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.03 % Allowed : 18.21 % Favored : 77.76 % 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 (0.20), residues: 1830 helix: 0.03 (0.18), residues: 800 sheet: 1.06 (0.29), residues: 330 loop : -0.03 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 340 HIS 0.007 0.002 HIS A 161 PHE 0.020 0.002 PHE C 127 TYR 0.010 0.002 TYR D 240 ARG 0.007 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 708) hydrogen bonds : angle 4.50974 ( 1863) covalent geometry : bond 0.00849 (14960) covalent geometry : angle 0.68738 (20305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 303 time to evaluate : 1.842 Fit side-chains REVERT: A 349 LEU cc_start: 0.8815 (mt) cc_final: 0.8501 (mp) REVERT: B 47 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.5933 (ppp) REVERT: B 82 MET cc_start: 0.8591 (tpt) cc_final: 0.8384 (tpt) REVERT: C 314 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: D 132 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8125 (ttp) REVERT: D 176 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.7882 (mtp) REVERT: D 299 MET cc_start: 0.8920 (mtm) cc_final: 0.8624 (mtm) REVERT: D 326 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7982 (mptp) REVERT: E 107 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7559 (tt0) outliers start: 63 outliers final: 35 residues processed: 332 average time/residue: 2.0070 time to fit residues: 716.7977 Evaluate side-chains 341 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 300 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 284 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 75 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 41 optimal weight: 0.0060 chunk 70 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 59 GLN B 246 GLN C 246 GLN C 263 GLN C 353 GLN D 162 ASN D 297 ASN D 353 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 297 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.108300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.100721 restraints weight = 19305.332| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.18 r_work: 0.3397 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14960 Z= 0.102 Angle : 0.545 6.153 20305 Z= 0.264 Chirality : 0.044 0.136 2255 Planarity : 0.004 0.067 2595 Dihedral : 6.364 92.401 2085 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.68 % Allowed : 20.38 % Favored : 76.93 % 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 (0.20), residues: 1830 helix: 0.49 (0.19), residues: 800 sheet: 1.03 (0.28), residues: 340 loop : 0.18 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS D 161 PHE 0.009 0.001 PHE B 127 TYR 0.006 0.001 TYR C 143 ARG 0.009 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 708) hydrogen bonds : angle 4.17875 ( 1863) covalent geometry : bond 0.00235 (14960) covalent geometry : angle 0.54459 (20305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 320 time to evaluate : 1.809 Fit side-chains REVERT: B 47 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.5965 (ppp) REVERT: B 78 ASN cc_start: 0.8284 (t0) cc_final: 0.8059 (t0) REVERT: C 6 THR cc_start: 0.8509 (p) cc_final: 0.8258 (t) REVERT: C 314 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7038 (tt0) REVERT: C 363 ASP cc_start: 0.8154 (m-30) cc_final: 0.7856 (m-30) REVERT: D 6 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7935 (t) REVERT: D 119 MET cc_start: 0.8413 (ttp) cc_final: 0.8171 (mtp) REVERT: D 299 MET cc_start: 0.8888 (mtm) cc_final: 0.8569 (mtm) REVERT: D 326 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8021 (mptp) REVERT: E 107 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: E 113 LYS cc_start: 0.8465 (mmmm) cc_final: 0.8162 (mptt) outliers start: 42 outliers final: 21 residues processed: 343 average time/residue: 1.7836 time to fit residues: 657.4072 Evaluate side-chains 339 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 313 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 2.9990 chunk 139 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 167 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 137 GLN A 297 ASN B 59 GLN C 246 GLN C 263 GLN C 353 GLN D 162 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.107451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.099945 restraints weight = 19292.796| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.16 r_work: 0.3390 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14960 Z= 0.130 Angle : 0.557 6.314 20305 Z= 0.271 Chirality : 0.045 0.135 2255 Planarity : 0.004 0.063 2595 Dihedral : 6.202 91.961 2085 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.68 % Allowed : 20.83 % Favored : 76.49 % 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: 0.73 (0.20), residues: 1830 helix: 0.66 (0.19), residues: 800 sheet: 1.02 (0.28), residues: 340 loop : 0.20 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 79 HIS 0.004 0.001 HIS D 161 PHE 0.011 0.001 PHE B 127 TYR 0.007 0.001 TYR C 188 ARG 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 708) hydrogen bonds : angle 4.13763 ( 1863) covalent geometry : bond 0.00312 (14960) covalent geometry : angle 0.55711 (20305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 315 time to evaluate : 2.992 Fit side-chains REVERT: B 78 ASN cc_start: 0.8289 (t0) cc_final: 0.8047 (t0) REVERT: C 6 THR cc_start: 0.8461 (p) cc_final: 0.8224 (t) REVERT: C 314 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7032 (tt0) REVERT: C 363 ASP cc_start: 0.8152 (m-30) cc_final: 0.7862 (m-30) REVERT: D 6 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7972 (t) REVERT: D 119 MET cc_start: 0.8405 (ttp) cc_final: 0.8166 (mtp) REVERT: D 132 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8110 (ttp) REVERT: D 176 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.7894 (mtp) REVERT: D 299 MET cc_start: 0.8898 (mtm) cc_final: 0.8584 (mtm) REVERT: E 107 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: E 113 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8196 (mptt) outliers start: 42 outliers final: 27 residues processed: 334 average time/residue: 2.1619 time to fit residues: 774.6051 Evaluate side-chains 340 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 308 time to evaluate : 3.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 130 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 145 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 137 GLN A 297 ASN B 59 GLN B 297 ASN C 246 GLN C 263 GLN C 353 GLN D 296 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.108349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.100900 restraints weight = 19295.620| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.16 r_work: 0.3406 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14960 Z= 0.107 Angle : 0.540 6.115 20305 Z= 0.261 Chirality : 0.044 0.131 2255 Planarity : 0.004 0.064 2595 Dihedral : 5.853 85.427 2085 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.94 % Allowed : 20.89 % Favored : 76.17 % 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: 0.89 (0.20), residues: 1830 helix: 0.82 (0.19), residues: 800 sheet: 1.05 (0.28), residues: 340 loop : 0.26 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 79 HIS 0.003 0.001 HIS D 161 PHE 0.009 0.001 PHE B 127 TYR 0.005 0.001 TYR A 69 ARG 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.02867 ( 708) hydrogen bonds : angle 4.06241 ( 1863) covalent geometry : bond 0.00252 (14960) covalent geometry : angle 0.54050 (20305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 319 time to evaluate : 2.016 Fit side-chains REVERT: A 136 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8379 (mp) REVERT: B 78 ASN cc_start: 0.8251 (t0) cc_final: 0.7988 (t0) REVERT: B 225 ASN cc_start: 0.8136 (m-40) cc_final: 0.7902 (m-40) REVERT: C 6 THR cc_start: 0.8465 (p) cc_final: 0.8238 (t) REVERT: C 363 ASP cc_start: 0.8138 (m-30) cc_final: 0.7850 (m-30) REVERT: D 119 MET cc_start: 0.8366 (ttp) cc_final: 0.8128 (mtp) REVERT: D 132 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8123 (ttp) REVERT: D 299 MET cc_start: 0.8840 (mtm) cc_final: 0.8518 (mtm) REVERT: E 107 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7297 (tt0) REVERT: E 113 LYS cc_start: 0.8481 (mmmm) cc_final: 0.8174 (mptt) outliers start: 46 outliers final: 23 residues processed: 342 average time/residue: 1.8127 time to fit residues: 664.5449 Evaluate side-chains 337 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 311 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 47 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 137 GLN A 297 ASN A 353 GLN B 59 GLN B 246 GLN B 297 ASN C 246 GLN C 263 GLN C 353 GLN D 296 ASN E 12 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.106852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.099379 restraints weight = 19061.460| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.14 r_work: 0.3375 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14960 Z= 0.208 Angle : 0.603 7.169 20305 Z= 0.296 Chirality : 0.048 0.150 2255 Planarity : 0.004 0.067 2595 Dihedral : 6.368 91.948 2085 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.68 % Allowed : 21.47 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1830 helix: 0.64 (0.19), residues: 800 sheet: 1.07 (0.28), residues: 330 loop : 0.15 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 340 HIS 0.005 0.001 HIS A 161 PHE 0.017 0.001 PHE B 127 TYR 0.008 0.001 TYR C 240 ARG 0.008 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 708) hydrogen bonds : angle 4.23569 ( 1863) covalent geometry : bond 0.00514 (14960) covalent geometry : angle 0.60273 (20305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 312 time to evaluate : 1.603 Fit side-chains REVERT: A 176 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8227 (mtt) REVERT: A 314 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: B 47 MET cc_start: 0.6771 (ppp) cc_final: 0.6056 (ppp) REVERT: B 78 ASN cc_start: 0.8305 (t0) cc_final: 0.8053 (t0) REVERT: C 363 ASP cc_start: 0.8158 (m-30) cc_final: 0.7881 (m-30) REVERT: D 119 MET cc_start: 0.8408 (ttp) cc_final: 0.8172 (mtp) REVERT: D 176 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.7925 (mtp) REVERT: D 299 MET cc_start: 0.8887 (mtm) cc_final: 0.8536 (mtm) REVERT: D 326 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8168 (mptp) REVERT: E 107 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: E 113 LYS cc_start: 0.8458 (mmmm) cc_final: 0.8196 (mptt) outliers start: 42 outliers final: 27 residues processed: 330 average time/residue: 1.7214 time to fit residues: 608.1352 Evaluate side-chains 338 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 306 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 155 optimal weight: 0.4980 chunk 154 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 162 ASN B 59 GLN B 297 ASN C 246 GLN C 263 GLN C 353 GLN D 115 ASN D 162 ASN D 296 ASN E 297 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.108335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.100845 restraints weight = 19052.606| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.16 r_work: 0.3400 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14960 Z= 0.116 Angle : 0.554 6.245 20305 Z= 0.269 Chirality : 0.045 0.131 2255 Planarity : 0.004 0.068 2595 Dihedral : 5.951 84.064 2085 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.43 % Allowed : 21.85 % Favored : 75.72 % 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: 0.84 (0.20), residues: 1830 helix: 0.82 (0.19), residues: 800 sheet: 0.99 (0.28), residues: 340 loop : 0.21 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS D 161 PHE 0.010 0.001 PHE B 127 TYR 0.006 0.001 TYR A 69 ARG 0.009 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03006 ( 708) hydrogen bonds : angle 4.11431 ( 1863) covalent geometry : bond 0.00277 (14960) covalent geometry : angle 0.55436 (20305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 313 time to evaluate : 1.705 Fit side-chains REVERT: A 314 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: B 47 MET cc_start: 0.6812 (ppp) cc_final: 0.6111 (ppp) REVERT: B 78 ASN cc_start: 0.8315 (t0) cc_final: 0.8071 (t0) REVERT: C 363 ASP cc_start: 0.8120 (m-30) cc_final: 0.7838 (m-30) REVERT: D 119 MET cc_start: 0.8446 (ttp) cc_final: 0.8214 (mtp) REVERT: D 176 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.7830 (mtp) REVERT: D 299 MET cc_start: 0.8864 (mtm) cc_final: 0.8503 (mtm) REVERT: E 107 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7327 (tt0) outliers start: 38 outliers final: 25 residues processed: 333 average time/residue: 1.6816 time to fit residues: 601.2761 Evaluate side-chains 336 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 308 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 52 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 137 GLN A 162 ASN A 353 GLN B 59 GLN B 297 ASN C 246 GLN C 263 GLN C 353 GLN D 115 ASN D 162 ASN D 296 ASN D 297 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.107577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.099999 restraints weight = 19091.983| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.18 r_work: 0.3385 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14960 Z= 0.162 Angle : 0.584 6.558 20305 Z= 0.285 Chirality : 0.047 0.131 2255 Planarity : 0.004 0.069 2595 Dihedral : 6.095 85.476 2085 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.17 % Allowed : 22.17 % Favored : 75.65 % 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: 0.78 (0.20), residues: 1830 helix: 0.79 (0.19), residues: 800 sheet: 0.95 (0.28), residues: 340 loop : 0.16 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 79 HIS 0.004 0.001 HIS A 161 PHE 0.014 0.001 PHE B 127 TYR 0.006 0.001 TYR C 240 ARG 0.010 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 708) hydrogen bonds : angle 4.15795 ( 1863) covalent geometry : bond 0.00397 (14960) covalent geometry : angle 0.58360 (20305) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 315 time to evaluate : 1.578 Fit side-chains REVERT: A 176 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8253 (mtt) REVERT: A 314 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: B 47 MET cc_start: 0.6826 (ppp) cc_final: 0.6144 (ppp) REVERT: B 78 ASN cc_start: 0.8357 (t0) cc_final: 0.8110 (t0) REVERT: C 147 ARG cc_start: 0.8827 (ptp-170) cc_final: 0.8594 (ptp-110) REVERT: C 363 ASP cc_start: 0.8133 (m-30) cc_final: 0.7848 (m-30) REVERT: D 119 MET cc_start: 0.8473 (ttp) cc_final: 0.8235 (mtp) REVERT: D 176 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.7900 (mtp) REVERT: D 299 MET cc_start: 0.8907 (mtm) cc_final: 0.8558 (mtm) REVERT: E 107 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: E 113 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8216 (mptt) outliers start: 34 outliers final: 27 residues processed: 335 average time/residue: 1.7215 time to fit residues: 617.1068 Evaluate side-chains 340 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 309 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 134 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 156 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 162 ASN B 59 GLN B 297 ASN C 246 GLN C 263 GLN C 353 GLN D 115 ASN D 162 ASN D 296 ASN D 297 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.108194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.100699 restraints weight = 19114.519| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.16 r_work: 0.3397 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14960 Z= 0.124 Angle : 0.564 6.303 20305 Z= 0.274 Chirality : 0.045 0.131 2255 Planarity : 0.004 0.069 2595 Dihedral : 5.956 83.209 2085 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.11 % Allowed : 22.49 % Favored : 75.40 % 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: 0.85 (0.20), residues: 1830 helix: 0.84 (0.19), residues: 800 sheet: 0.97 (0.28), residues: 340 loop : 0.22 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.004 0.001 HIS D 161 PHE 0.011 0.001 PHE B 127 TYR 0.006 0.001 TYR C 240 ARG 0.009 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 708) hydrogen bonds : angle 4.10101 ( 1863) covalent geometry : bond 0.00297 (14960) covalent geometry : angle 0.56359 (20305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15650.70 seconds wall clock time: 274 minutes 15.49 seconds (16455.49 seconds total)