Starting phenix.real_space_refine on Wed Mar 4 13:38:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ckw_30392/03_2026/7ckw_30392.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ckw_30392/03_2026/7ckw_30392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ckw_30392/03_2026/7ckw_30392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ckw_30392/03_2026/7ckw_30392.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ckw_30392/03_2026/7ckw_30392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ckw_30392/03_2026/7ckw_30392.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7222 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 53 5.16 5 Cl 1 4.86 5 C 5158 2.51 5 N 1403 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8103 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1906 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2587 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2153 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 263} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'CLR': 1, 'G3C': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.89, per 1000 atoms: 0.23 Number of scatterers: 8103 At special positions: 0 Unit cell: (89, 87, 123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 53 16.00 O 1488 8.00 N 1403 7.00 C 5158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 313.2 milliseconds 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 42.1% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.709A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 254 through 255 No H-bonds generated for 'chain 'A' and resid 254 through 255' Processing helix chain 'A' and resid 263 through 263 No H-bonds generated for 'chain 'A' and resid 263 through 263' Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.223A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.961A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.643A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.604A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.512A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.651A pdb=" N ILE B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'R' and resid 22 through 50 removed outlier: 4.616A pdb=" N THR R 26 " --> pdb=" O VAL R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 77 removed outlier: 3.707A pdb=" N PHE R 61 " --> pdb=" O LYS R 57 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 86 removed outlier: 3.512A pdb=" N LYS R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 94 No H-bonds generated for 'chain 'R' and resid 92 through 94' Processing helix chain 'R' and resid 95 through 126 removed outlier: 4.502A pdb=" N ALA R 109 " --> pdb=" O MET R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 161 removed outlier: 4.108A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 191 through 203 removed outlier: 3.904A pdb=" N SER R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE R 201 " --> pdb=" O SER R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 237 removed outlier: 3.849A pdb=" N ALA R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 278 removed outlier: 3.576A pdb=" N LYS R 269 " --> pdb=" O LYS R 265 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL R 270 " --> pdb=" O ARG R 266 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 293 Proline residue: R 287 - end of helix removed outlier: 4.076A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 331 removed outlier: 4.058A pdb=" N ASP R 314 " --> pdb=" O SER R 310 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 344 removed outlier: 3.781A pdb=" N ALA R 340 " --> pdb=" O ASP R 336 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR R 343 " --> pdb=" O LYS R 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.575A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 removed outlier: 7.007A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.599A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 4.082A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.941A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.518A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.519A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.592A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.675A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1182 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: 1.49 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2630 1.34 - 1.46: 1961 1.46 - 1.58: 3610 1.58 - 1.69: 0 1.69 - 1.81: 73 Bond restraints: 8274 Sorted by residual: bond pdb=" C02 G3C R 501 " pdb=" O01 G3C R 501 " ideal model delta sigma weight residual 1.345 1.399 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" C11 G3C R 501 " pdb=" O12 G3C R 501 " ideal model delta sigma weight residual 1.349 1.402 -0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" N HIS A 357 " pdb=" CA HIS A 357 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 7.01e+00 bond pdb=" N PHE B 234 " pdb=" CA PHE B 234 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.30e-02 5.92e+03 6.21e+00 bond pdb=" C03 G3C R 501 " pdb=" O04 G3C R 501 " ideal model delta sigma weight residual 1.352 1.400 -0.048 2.00e-02 2.50e+03 5.72e+00 ... (remaining 8269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 10777 1.07 - 2.14: 371 2.14 - 3.20: 56 3.20 - 4.27: 15 4.27 - 5.34: 9 Bond angle restraints: 11228 Sorted by residual: angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 126.27 -4.73 1.91e+00 2.74e-01 6.14e+00 angle pdb=" N VAL R 75 " pdb=" CA VAL R 75 " pdb=" C VAL R 75 " ideal model delta sigma weight residual 113.42 111.12 2.30 1.17e+00 7.31e-01 3.86e+00 angle pdb=" CA VAL R 75 " pdb=" C VAL R 75 " pdb=" N LEU R 76 " ideal model delta sigma weight residual 118.90 117.20 1.70 9.40e-01 1.13e+00 3.28e+00 angle pdb=" CA VAL R 75 " pdb=" C VAL R 75 " pdb=" O VAL R 75 " ideal model delta sigma weight residual 118.90 120.45 -1.55 8.80e-01 1.29e+00 3.11e+00 angle pdb=" C LEU B 79 " pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta sigma weight residual 122.90 120.65 2.25 1.28e+00 6.10e-01 3.09e+00 ... (remaining 11223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4466 17.29 - 34.57: 394 34.57 - 51.86: 89 51.86 - 69.14: 13 69.14 - 86.43: 4 Dihedral angle restraints: 4966 sinusoidal: 1950 harmonic: 3016 Sorted by residual: dihedral pdb=" CB CYS R 298 " pdb=" SG CYS R 298 " pdb=" SG CYS R 307 " pdb=" CB CYS R 307 " ideal model delta sinusoidal sigma weight residual 93.00 32.63 60.37 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CA ASP B 212 " pdb=" CB ASP B 212 " pdb=" CG ASP B 212 " pdb=" OD1 ASP B 212 " ideal model delta sinusoidal sigma weight residual -30.00 -82.75 52.75 1 2.00e+01 2.50e-03 9.47e+00 dihedral pdb=" CB MET B 217 " pdb=" CG MET B 217 " pdb=" SD MET B 217 " pdb=" CE MET B 217 " ideal model delta sinusoidal sigma weight residual -180.00 -122.55 -57.45 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 4963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1090 0.055 - 0.109: 178 0.109 - 0.164: 10 0.164 - 0.219: 0 0.219 - 0.273: 1 Chirality restraints: 1279 Sorted by residual: chirality pdb=" C07 G3C R 501 " pdb=" C06 G3C R 501 " pdb=" C08 G3C R 501 " pdb=" C15 G3C R 501 " both_signs ideal model delta sigma weight residual False -2.44 -2.71 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA VAL B 296 " pdb=" N VAL B 296 " pdb=" C VAL B 296 " pdb=" CB VAL B 296 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 1276 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 114 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C LEU R 114 " 0.024 2.00e-02 2.50e+03 pdb=" O LEU R 114 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS R 115 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 104 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C ILE R 104 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE R 104 " -0.009 2.00e-02 2.50e+03 pdb=" N MET R 105 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 205 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO R 206 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO R 206 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 206 " -0.019 5.00e-02 4.00e+02 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 398 2.72 - 3.27: 8597 3.27 - 3.81: 14796 3.81 - 4.36: 18166 4.36 - 4.90: 30203 Nonbonded interactions: 72160 Sorted by model distance: nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.178 3.040 nonbonded pdb=" OG SER R 199 " pdb=" ND2 ASN R 292 " model vdw 2.179 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.186 3.040 nonbonded pdb=" CG1 VAL B 200 " pdb=" CE2 PHE B 234 " model vdw 2.200 3.760 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.222 3.040 ... (remaining 72155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 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 : 0.002 0.054 8278 Z= 0.139 Angle : 0.480 5.340 11236 Z= 0.288 Chirality : 0.039 0.273 1279 Planarity : 0.003 0.033 1418 Dihedral : 13.674 86.426 2994 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.74 % Allowed : 12.33 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.23), residues: 1015 helix: -1.57 (0.22), residues: 383 sheet: -2.85 (0.32), residues: 188 loop : -2.31 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.009 0.001 TYR N 117 PHE 0.006 0.001 PHE B 235 TRP 0.010 0.001 TRP B 82 HIS 0.001 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8274) covalent geometry : angle 0.48022 (11228) SS BOND : bond 0.00165 ( 4) SS BOND : angle 0.55722 ( 8) hydrogen bonds : bond 0.19401 ( 410) hydrogen bonds : angle 7.66599 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 276 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.4469 (t80) cc_final: 0.3946 (t80) REVERT: B 150 ARG cc_start: 0.8555 (mmt-90) cc_final: 0.6650 (mmt90) REVERT: B 313 ASN cc_start: 0.8331 (t0) cc_final: 0.7937 (t0) REVERT: N 32 TYR cc_start: 0.8558 (m-80) cc_final: 0.8277 (m-80) REVERT: N 35 ASN cc_start: 0.7138 (p0) cc_final: 0.6919 (p0) REVERT: R 105 MET cc_start: 0.6811 (ttp) cc_final: 0.6604 (tmm) REVERT: R 125 ILE cc_start: 0.8110 (mm) cc_final: 0.7607 (mm) REVERT: R 154 ILE cc_start: 0.8044 (tp) cc_final: 0.7783 (tp) outliers start: 15 outliers final: 5 residues processed: 286 average time/residue: 0.1091 time to fit residues: 40.0991 Evaluate side-chains 217 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 212 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 136 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 220 HIS A 278 ASN A 371 ASN B 32 GLN B 125 ASN B 237 ASN B 266 HIS B 340 ASN N 84 ASN N 120 GLN N 123 GLN R 60 ASN R 323 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.204467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.167794 restraints weight = 9304.246| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.26 r_work: 0.3718 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8278 Z= 0.177 Angle : 0.573 6.991 11236 Z= 0.300 Chirality : 0.043 0.228 1279 Planarity : 0.005 0.053 1418 Dihedral : 5.162 49.764 1208 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.30 % Allowed : 17.44 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.25), residues: 1015 helix: 0.05 (0.26), residues: 389 sheet: -2.71 (0.33), residues: 186 loop : -1.78 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 374 TYR 0.012 0.001 TYR R 331 PHE 0.026 0.002 PHE B 241 TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8274) covalent geometry : angle 0.57175 (11228) SS BOND : bond 0.00516 ( 4) SS BOND : angle 1.48340 ( 8) hydrogen bonds : bond 0.04744 ( 410) hydrogen bonds : angle 5.64275 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5164 (t80) cc_final: 0.4101 (t80) REVERT: A 270 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8599 (mp) REVERT: A 292 ASN cc_start: 0.8163 (t0) cc_final: 0.7869 (t0) REVERT: A 389 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.7716 (tpt170) REVERT: B 111 TYR cc_start: 0.8195 (m-80) cc_final: 0.7638 (m-80) REVERT: B 283 ARG cc_start: 0.8535 (tpt170) cc_final: 0.8291 (tpp80) REVERT: B 321 THR cc_start: 0.7582 (p) cc_final: 0.7335 (p) REVERT: N 32 TYR cc_start: 0.8966 (m-80) cc_final: 0.8706 (m-80) REVERT: N 65 LYS cc_start: 0.8186 (tptm) cc_final: 0.7855 (tppt) REVERT: R 105 MET cc_start: 0.7693 (ttp) cc_final: 0.6905 (tpt) REVERT: R 154 ILE cc_start: 0.8084 (tp) cc_final: 0.7751 (tp) outliers start: 37 outliers final: 19 residues processed: 264 average time/residue: 0.0871 time to fit residues: 31.0888 Evaluate side-chains 239 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 236 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 60 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 267 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.201248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.163650 restraints weight = 9128.181| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.28 r_work: 0.3680 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8278 Z= 0.178 Angle : 0.587 8.360 11236 Z= 0.300 Chirality : 0.043 0.146 1279 Planarity : 0.004 0.054 1418 Dihedral : 4.859 54.580 1206 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.00 % Allowed : 20.58 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.26), residues: 1015 helix: 0.31 (0.26), residues: 395 sheet: -2.47 (0.33), residues: 190 loop : -1.57 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 52 TYR 0.009 0.001 TYR B 124 PHE 0.016 0.001 PHE B 241 TRP 0.010 0.002 TRP A 281 HIS 0.010 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8274) covalent geometry : angle 0.58454 (11228) SS BOND : bond 0.00355 ( 4) SS BOND : angle 2.07724 ( 8) hydrogen bonds : bond 0.04317 ( 410) hydrogen bonds : angle 5.50793 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5145 (t80) cc_final: 0.4274 (t80) REVERT: A 270 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8781 (mp) REVERT: A 292 ASN cc_start: 0.8276 (t0) cc_final: 0.8014 (t0) REVERT: A 318 TYR cc_start: 0.6775 (t80) cc_final: 0.6417 (t80) REVERT: B 52 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.6909 (ptp-170) REVERT: B 111 TYR cc_start: 0.8198 (m-80) cc_final: 0.7783 (m-80) REVERT: B 225 HIS cc_start: 0.8096 (OUTLIER) cc_final: 0.7869 (t-90) REVERT: B 245 SER cc_start: 0.9021 (p) cc_final: 0.8670 (p) REVERT: B 297 TRP cc_start: 0.8499 (m100) cc_final: 0.8298 (m100) REVERT: B 321 THR cc_start: 0.7689 (p) cc_final: 0.7406 (p) REVERT: N 32 TYR cc_start: 0.9083 (m-80) cc_final: 0.8804 (m-80) REVERT: N 33 LYS cc_start: 0.8596 (tttm) cc_final: 0.8237 (tmtt) REVERT: R 154 ILE cc_start: 0.8185 (tp) cc_final: 0.7868 (tp) outliers start: 43 outliers final: 28 residues processed: 265 average time/residue: 0.0869 time to fit residues: 31.2766 Evaluate side-chains 255 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 38 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 271 ASN N 53 GLN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.198816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.162909 restraints weight = 9233.886| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.21 r_work: 0.3690 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8278 Z= 0.152 Angle : 0.567 8.871 11236 Z= 0.289 Chirality : 0.042 0.140 1279 Planarity : 0.004 0.050 1418 Dihedral : 5.063 55.993 1206 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.65 % Allowed : 21.16 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.26), residues: 1015 helix: 0.51 (0.26), residues: 395 sheet: -2.35 (0.34), residues: 189 loop : -1.42 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 214 TYR 0.017 0.001 TYR R 331 PHE 0.013 0.001 PHE B 241 TRP 0.013 0.001 TRP B 99 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8274) covalent geometry : angle 0.56445 (11228) SS BOND : bond 0.00295 ( 4) SS BOND : angle 1.91992 ( 8) hydrogen bonds : bond 0.03960 ( 410) hydrogen bonds : angle 5.38395 ( 1182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5146 (t80) cc_final: 0.4321 (t80) REVERT: A 292 ASN cc_start: 0.7946 (t0) cc_final: 0.7606 (t0) REVERT: A 318 TYR cc_start: 0.6852 (t80) cc_final: 0.6620 (t80) REVERT: B 111 TYR cc_start: 0.8160 (m-80) cc_final: 0.7742 (m-80) REVERT: B 245 SER cc_start: 0.8955 (p) cc_final: 0.8641 (p) REVERT: B 283 ARG cc_start: 0.8329 (tpt170) cc_final: 0.8076 (tpt170) REVERT: B 321 THR cc_start: 0.7791 (p) cc_final: 0.7562 (p) REVERT: G 29 LYS cc_start: 0.8891 (tptm) cc_final: 0.8684 (tptp) REVERT: N 33 LYS cc_start: 0.8569 (tttm) cc_final: 0.8221 (tmtt) REVERT: R 60 ASN cc_start: 0.7737 (m-40) cc_final: 0.7373 (m110) REVERT: R 154 ILE cc_start: 0.8163 (tp) cc_final: 0.7795 (tp) REVERT: R 156 PHE cc_start: 0.7733 (m-10) cc_final: 0.7507 (m-80) outliers start: 40 outliers final: 28 residues processed: 255 average time/residue: 0.0904 time to fit residues: 31.0557 Evaluate side-chains 239 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 60 optimal weight: 0.7980 chunk 26 optimal weight: 40.0000 chunk 90 optimal weight: 0.0670 chunk 81 optimal weight: 0.4980 chunk 57 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN N 53 GLN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.199104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161133 restraints weight = 9174.470| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.30 r_work: 0.3658 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 8278 Z= 0.182 Angle : 0.614 9.791 11236 Z= 0.309 Chirality : 0.043 0.154 1279 Planarity : 0.004 0.045 1418 Dihedral : 5.258 57.965 1206 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.81 % Allowed : 21.63 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.26), residues: 1015 helix: 0.56 (0.26), residues: 395 sheet: -2.42 (0.33), residues: 204 loop : -1.19 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 214 TYR 0.012 0.002 TYR N 115 PHE 0.010 0.001 PHE B 241 TRP 0.015 0.002 TRP B 99 HIS 0.007 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8274) covalent geometry : angle 0.60496 (11228) SS BOND : bond 0.01110 ( 4) SS BOND : angle 3.93159 ( 8) hydrogen bonds : bond 0.03975 ( 410) hydrogen bonds : angle 5.29751 ( 1182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5445 (t80) cc_final: 0.4544 (t80) REVERT: A 292 ASN cc_start: 0.7994 (t0) cc_final: 0.7652 (t0) REVERT: B 111 TYR cc_start: 0.8245 (m-80) cc_final: 0.7874 (m-80) REVERT: B 126 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7979 (mp) REVERT: B 168 LEU cc_start: 0.8554 (tp) cc_final: 0.8250 (tp) REVERT: B 321 THR cc_start: 0.7969 (p) cc_final: 0.7730 (p) REVERT: B 334 SER cc_start: 0.8566 (OUTLIER) cc_final: 0.8138 (t) REVERT: N 33 LYS cc_start: 0.8444 (tttm) cc_final: 0.7791 (tmtt) REVERT: R 154 ILE cc_start: 0.8194 (tp) cc_final: 0.7808 (tp) REVERT: R 156 PHE cc_start: 0.7896 (m-10) cc_final: 0.7650 (m-80) outliers start: 50 outliers final: 30 residues processed: 252 average time/residue: 0.0940 time to fit residues: 31.9698 Evaluate side-chains 239 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.3980 chunk 96 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 293 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.201172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.163880 restraints weight = 9145.278| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.27 r_work: 0.3698 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 8278 Z= 0.165 Angle : 0.622 11.166 11236 Z= 0.309 Chirality : 0.043 0.160 1279 Planarity : 0.004 0.048 1418 Dihedral : 4.986 59.445 1203 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.23 % Allowed : 22.79 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.26), residues: 1015 helix: 0.56 (0.26), residues: 399 sheet: -2.24 (0.33), residues: 214 loop : -1.20 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 214 TYR 0.014 0.002 TYR B 264 PHE 0.023 0.001 PHE B 292 TRP 0.016 0.002 TRP B 99 HIS 0.007 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8274) covalent geometry : angle 0.61623 (11228) SS BOND : bond 0.00423 ( 4) SS BOND : angle 3.31489 ( 8) hydrogen bonds : bond 0.03849 ( 410) hydrogen bonds : angle 5.26259 ( 1182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 218 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5288 (t80) cc_final: 0.4393 (t80) REVERT: A 292 ASN cc_start: 0.7997 (t0) cc_final: 0.7665 (t0) REVERT: B 111 TYR cc_start: 0.8192 (m-80) cc_final: 0.7798 (m-80) REVERT: B 126 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7882 (mp) REVERT: B 168 LEU cc_start: 0.8551 (tp) cc_final: 0.8308 (tp) REVERT: B 314 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7706 (ttp-170) REVERT: B 321 THR cc_start: 0.7988 (p) cc_final: 0.7752 (p) REVERT: G 29 LYS cc_start: 0.8673 (tptp) cc_final: 0.8198 (tptt) REVERT: N 33 LYS cc_start: 0.8634 (tttm) cc_final: 0.7930 (tmtt) REVERT: R 154 ILE cc_start: 0.8160 (tp) cc_final: 0.7769 (tp) REVERT: R 156 PHE cc_start: 0.7835 (m-10) cc_final: 0.7591 (m-80) outliers start: 45 outliers final: 31 residues processed: 249 average time/residue: 0.0853 time to fit residues: 28.9320 Evaluate side-chains 243 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 68 optimal weight: 0.0570 chunk 25 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.201753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.164774 restraints weight = 9244.499| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.29 r_work: 0.3692 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8278 Z= 0.150 Angle : 0.609 11.365 11236 Z= 0.303 Chirality : 0.043 0.141 1279 Planarity : 0.004 0.062 1418 Dihedral : 4.968 58.114 1203 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.30 % Allowed : 24.42 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.26), residues: 1015 helix: 0.67 (0.26), residues: 396 sheet: -2.08 (0.34), residues: 202 loop : -1.16 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 214 TYR 0.008 0.001 TYR N 115 PHE 0.023 0.001 PHE B 292 TRP 0.014 0.002 TRP A 281 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8274) covalent geometry : angle 0.60538 (11228) SS BOND : bond 0.00319 ( 4) SS BOND : angle 2.46219 ( 8) hydrogen bonds : bond 0.03725 ( 410) hydrogen bonds : angle 5.19930 ( 1182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5398 (t80) cc_final: 0.4542 (t80) REVERT: A 292 ASN cc_start: 0.7998 (t0) cc_final: 0.7683 (t0) REVERT: B 111 TYR cc_start: 0.8164 (m-80) cc_final: 0.7705 (m-80) REVERT: B 126 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7847 (mp) REVERT: G 29 LYS cc_start: 0.8697 (tptp) cc_final: 0.8201 (tptt) REVERT: N 33 LYS cc_start: 0.8654 (tttm) cc_final: 0.7954 (tmtt) REVERT: R 60 ASN cc_start: 0.8021 (m-40) cc_final: 0.7685 (m110) REVERT: R 71 LEU cc_start: 0.7632 (mp) cc_final: 0.7339 (mp) REVERT: R 123 TRP cc_start: 0.7688 (m100) cc_final: 0.7196 (m100) REVERT: R 154 ILE cc_start: 0.8034 (tp) cc_final: 0.7787 (tp) REVERT: R 156 PHE cc_start: 0.7822 (m-10) cc_final: 0.7573 (m-80) outliers start: 37 outliers final: 29 residues processed: 238 average time/residue: 0.0851 time to fit residues: 27.7864 Evaluate side-chains 233 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 94 optimal weight: 0.0070 chunk 3 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 293 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.210186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.174543 restraints weight = 9009.082| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.21 r_work: 0.3833 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8278 Z= 0.142 Angle : 0.601 11.963 11236 Z= 0.301 Chirality : 0.043 0.141 1279 Planarity : 0.004 0.042 1418 Dihedral : 4.975 58.090 1203 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.00 % Allowed : 24.53 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.27), residues: 1015 helix: 0.67 (0.26), residues: 401 sheet: -2.06 (0.34), residues: 203 loop : -1.11 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.013 0.002 TYR R 218 PHE 0.023 0.001 PHE B 292 TRP 0.014 0.002 TRP N 47 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8274) covalent geometry : angle 0.59831 (11228) SS BOND : bond 0.00246 ( 4) SS BOND : angle 2.04686 ( 8) hydrogen bonds : bond 0.03631 ( 410) hydrogen bonds : angle 5.14187 ( 1182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5511 (t80) cc_final: 0.4648 (t80) REVERT: A 292 ASN cc_start: 0.7886 (t0) cc_final: 0.7548 (t0) REVERT: B 111 TYR cc_start: 0.8105 (m-80) cc_final: 0.7685 (m-80) REVERT: B 314 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7679 (ttp-170) REVERT: G 29 LYS cc_start: 0.8715 (tptp) cc_final: 0.8260 (tptt) REVERT: N 33 LYS cc_start: 0.8636 (tttm) cc_final: 0.7924 (tmtt) REVERT: R 32 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7759 (tt) REVERT: R 154 ILE cc_start: 0.7975 (tp) cc_final: 0.7737 (tp) REVERT: R 156 PHE cc_start: 0.7730 (m-10) cc_final: 0.7473 (m-80) outliers start: 43 outliers final: 30 residues processed: 238 average time/residue: 0.0847 time to fit residues: 27.7101 Evaluate side-chains 236 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 293 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN ** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.203296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.166194 restraints weight = 9096.715| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.26 r_work: 0.3725 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8278 Z= 0.155 Angle : 0.619 10.995 11236 Z= 0.310 Chirality : 0.043 0.147 1279 Planarity : 0.004 0.057 1418 Dihedral : 4.991 56.219 1203 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.00 % Allowed : 24.42 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.27), residues: 1015 helix: 0.67 (0.26), residues: 402 sheet: -2.00 (0.34), residues: 209 loop : -1.06 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 197 TYR 0.011 0.001 TYR B 289 PHE 0.022 0.001 PHE B 292 TRP 0.020 0.002 TRP B 99 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8274) covalent geometry : angle 0.61705 (11228) SS BOND : bond 0.00224 ( 4) SS BOND : angle 1.99150 ( 8) hydrogen bonds : bond 0.03689 ( 410) hydrogen bonds : angle 5.15313 ( 1182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5321 (t80) cc_final: 0.4606 (t80) REVERT: A 292 ASN cc_start: 0.7970 (t0) cc_final: 0.7632 (t0) REVERT: B 99 TRP cc_start: 0.7146 (m-90) cc_final: 0.6911 (m100) REVERT: B 111 TYR cc_start: 0.8189 (m-80) cc_final: 0.7731 (m-80) REVERT: G 29 LYS cc_start: 0.8657 (tptp) cc_final: 0.8198 (tptt) REVERT: N 33 LYS cc_start: 0.8655 (tttm) cc_final: 0.8108 (tmtt) REVERT: R 32 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7816 (tt) REVERT: R 81 LYS cc_start: 0.8390 (tppt) cc_final: 0.8104 (tppt) REVERT: R 123 TRP cc_start: 0.7690 (m100) cc_final: 0.7203 (m100) REVERT: R 154 ILE cc_start: 0.7965 (tp) cc_final: 0.7706 (tp) REVERT: R 156 PHE cc_start: 0.7893 (m-10) cc_final: 0.7643 (m-80) outliers start: 43 outliers final: 36 residues processed: 237 average time/residue: 0.0918 time to fit residues: 29.5399 Evaluate side-chains 239 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 329 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 292 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 293 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN ** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.196696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.158135 restraints weight = 9176.551| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.29 r_work: 0.3619 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8278 Z= 0.240 Angle : 0.678 12.613 11236 Z= 0.341 Chirality : 0.045 0.177 1279 Planarity : 0.005 0.051 1418 Dihedral : 5.114 51.018 1203 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.53 % Allowed : 24.77 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.27), residues: 1015 helix: 0.54 (0.26), residues: 401 sheet: -2.13 (0.34), residues: 211 loop : -1.17 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 197 TYR 0.019 0.002 TYR B 264 PHE 0.023 0.002 PHE B 292 TRP 0.016 0.002 TRP A 277 HIS 0.009 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 8274) covalent geometry : angle 0.67474 (11228) SS BOND : bond 0.00299 ( 4) SS BOND : angle 2.42897 ( 8) hydrogen bonds : bond 0.04064 ( 410) hydrogen bonds : angle 5.35751 ( 1182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5515 (t80) cc_final: 0.4820 (t80) REVERT: A 292 ASN cc_start: 0.8067 (t0) cc_final: 0.7751 (t0) REVERT: B 8 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7564 (ptm-80) REVERT: B 111 TYR cc_start: 0.8345 (m-80) cc_final: 0.7924 (m-80) REVERT: B 274 THR cc_start: 0.8283 (p) cc_final: 0.8055 (p) REVERT: G 29 LYS cc_start: 0.8707 (tptp) cc_final: 0.8250 (tptt) REVERT: N 33 LYS cc_start: 0.8714 (tttm) cc_final: 0.8092 (tmtt) REVERT: R 32 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7830 (tt) REVERT: R 60 ASN cc_start: 0.8145 (m-40) cc_final: 0.7923 (m110) REVERT: R 81 LYS cc_start: 0.8431 (tppt) cc_final: 0.8139 (tppt) REVERT: R 123 TRP cc_start: 0.7736 (m100) cc_final: 0.7177 (m100) REVERT: R 154 ILE cc_start: 0.8035 (tp) cc_final: 0.7794 (tp) outliers start: 39 outliers final: 33 residues processed: 228 average time/residue: 0.0913 time to fit residues: 28.0284 Evaluate side-chains 232 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 268 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.200256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.162713 restraints weight = 9144.051| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.27 r_work: 0.3666 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8278 Z= 0.169 Angle : 0.650 12.436 11236 Z= 0.326 Chirality : 0.044 0.171 1279 Planarity : 0.004 0.042 1418 Dihedral : 5.173 43.587 1203 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.84 % Allowed : 25.81 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.26), residues: 1015 helix: 0.51 (0.26), residues: 402 sheet: -2.09 (0.34), residues: 211 loop : -1.13 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 214 TYR 0.012 0.002 TYR B 289 PHE 0.022 0.002 PHE B 292 TRP 0.021 0.002 TRP B 99 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8274) covalent geometry : angle 0.64789 (11228) SS BOND : bond 0.00212 ( 4) SS BOND : angle 2.10469 ( 8) hydrogen bonds : bond 0.03817 ( 410) hydrogen bonds : angle 5.28753 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1911.17 seconds wall clock time: 33 minutes 34.39 seconds (2014.39 seconds total)