Starting phenix.real_space_refine on Sat Sep 12 05:31:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ckw_30392/09_2026/7ckw_30392.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ckw_30392/09_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_30392/09_2026/7ckw_30392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ckw_30392/09_2026/7ckw_30392.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ckw_30392/09_2026/7ckw_30392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ckw_30392/09_2026/7ckw_30392.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ckw_30392/09_2026/7ckw_30392.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ckw_30392/09_2026/7ckw_30392.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.80, per 1000 atoms: 0.22 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: 0.79 Conformation dependent library (CDL) restraints added in 251.9 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: 0.21 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: 1.35 Time building geometry restraints manager: 0.98 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: 4401 17.29 - 34.57: 390 34.57 - 51.86: 87 51.86 - 69.14: 13 69.14 - 86.43: 4 Dihedral angle restraints: 4895 sinusoidal: 1879 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 4892 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 9.060 Find NCS groups from input model: 0.040 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 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 : 13.744 86.426 2923 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/Z covalent geometry : bond 0.00247 / 0.14 ( 8274) covalent geometry : angle 0.48022 / 0.29 (11228) SS BOND : bond 0.00165 / 0.08 ( 4) SS BOND : angle 0.55722 / 0.32 ( 8) hydrogen bonds : bond 0.19401 / 13.14 ( 410) hydrogen bonds : angle 7.66599 / 5.39 ( 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 : 0.283 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: 0.1134 time to fit residues: 41.9797 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 : 0.313 ------------------------------------------------------------------------------- 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... 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 = 0.4270 r_free = 0.4270 target = 0.204360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.167681 restraints weight = 9296.885| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.25 r_work: 0.3737 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8278 Z= 0.177 Angle : 0.573 7.086 11236 Z= 0.300 Chirality : 0.043 0.192 1279 Planarity : 0.005 0.052 1418 Dihedral : 4.857 50.367 1137 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.19 % Allowed : 17.67 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.92 (0.25), residues: 1015 helix: 0.05 (0.26), residues: 390 sheet: -2.70 (0.33), residues: 186 loop : -1.76 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 374 TYR 0.012 0.001 TYR R 331 PHE 0.026 0.002 PHE B 241 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 8274) covalent geometry : angle 0.57166 / 0.30 (11228) SS BOND : bond 0.00561 / 0.28 ( 4) SS BOND : angle 1.42585 / 0.82 ( 8) hydrogen bonds : bond 0.04729 / 3.21 ( 410) hydrogen bonds : angle 5.62375 / 3.94 ( 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 271 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5174 (t80) cc_final: 0.4109 (t80) REVERT: A 270 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8640 (mp) REVERT: A 292 ASN cc_start: 0.8068 (t0) cc_final: 0.7773 (t0) REVERT: A 389 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.7705 (tpt170) REVERT: B 111 TYR cc_start: 0.8186 (m-80) cc_final: 0.7644 (m-80) REVERT: B 283 ARG cc_start: 0.8543 (tpt170) cc_final: 0.8313 (tpp80) REVERT: B 321 THR cc_start: 0.7630 (p) cc_final: 0.7371 (p) REVERT: N 32 TYR cc_start: 0.8961 (m-80) cc_final: 0.8630 (m-80) REVERT: R 154 ILE cc_start: 0.8068 (tp) cc_final: 0.7743 (tp) outliers start: 36 outliers final: 19 residues processed: 262 average time/residue: 0.0914 time to fit residues: 32.4724 Evaluate side-chains 240 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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: 7.9990 chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN A 267 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.199014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160991 restraints weight = 9124.179| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.26 r_work: 0.3667 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8278 Z= 0.208 Angle : 0.607 8.405 11236 Z= 0.311 Chirality : 0.043 0.147 1279 Planarity : 0.004 0.054 1418 Dihedral : 5.097 55.005 1135 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.42 % Allowed : 21.28 % Favored : 74.30 % 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: -1.66 (0.26), residues: 1015 helix: 0.31 (0.26), residues: 394 sheet: -2.55 (0.33), residues: 194 loop : -1.64 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 214 TYR 0.009 0.002 TYR B 264 PHE 0.015 0.002 PHE B 241 TRP 0.011 0.002 TRP A 277 HIS 0.009 0.002 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 ( 8274) covalent geometry : angle 0.60423 / 0.31 (11228) SS BOND : bond 0.00453 / 0.23 ( 4) SS BOND : angle 2.15551 / 1.21 ( 8) hydrogen bonds : bond 0.04431 / 2.95 ( 410) hydrogen bonds : angle 5.54939 / 3.89 ( 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 279 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5199 (t80) cc_final: 0.4326 (t80) REVERT: A 270 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8889 (mp) REVERT: A 292 ASN cc_start: 0.8196 (t0) cc_final: 0.7953 (t0) REVERT: B 52 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7163 (ptp-170) REVERT: B 111 TYR cc_start: 0.8240 (m-80) cc_final: 0.7812 (m-80) REVERT: B 225 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7892 (t-90) REVERT: B 245 SER cc_start: 0.9028 (p) cc_final: 0.8742 (p) REVERT: B 297 TRP cc_start: 0.8589 (m100) cc_final: 0.8338 (m100) REVERT: B 321 THR cc_start: 0.7738 (p) cc_final: 0.7452 (p) REVERT: N 32 TYR cc_start: 0.9112 (m-80) cc_final: 0.8813 (m-80) REVERT: N 33 LYS cc_start: 0.8687 (tttm) cc_final: 0.8025 (tmtt) REVERT: R 60 ASN cc_start: 0.7762 (m-40) cc_final: 0.7407 (m110) REVERT: R 154 ILE cc_start: 0.8239 (tp) cc_final: 0.7909 (tp) outliers start: 38 outliers final: 26 residues processed: 265 average time/residue: 0.0938 time to fit residues: 33.6877 Evaluate side-chains 253 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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 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 73 VAL 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: 1.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 0.0670 chunk 83 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4250 r_free = 0.4250 target = 0.202016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.164924 restraints weight = 9266.155| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.26 r_work: 0.3717 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8278 Z= 0.143 Angle : 0.569 8.897 11236 Z= 0.289 Chirality : 0.042 0.147 1279 Planarity : 0.004 0.048 1418 Dihedral : 5.050 58.421 1133 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.53 % Allowed : 21.40 % Favored : 74.07 % 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: -1.31 (0.26), residues: 1015 helix: 0.48 (0.26), residues: 397 sheet: -2.31 (0.35), residues: 189 loop : -1.38 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 214 TYR 0.016 0.001 TYR R 331 PHE 0.013 0.001 PHE B 241 TRP 0.013 0.001 TRP B 99 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 8274) covalent geometry : angle 0.56725 / 0.29 (11228) SS BOND : bond 0.00271 / 0.14 ( 4) SS BOND : angle 1.82546 / 1.03 ( 8) hydrogen bonds : bond 0.03925 / 2.62 ( 410) hydrogen bonds : angle 5.37857 / 3.77 ( 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 272 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5242 (t80) cc_final: 0.4393 (t80) REVERT: A 292 ASN cc_start: 0.7968 (t0) cc_final: 0.7620 (t0) REVERT: A 318 TYR cc_start: 0.6825 (t80) cc_final: 0.6610 (t80) REVERT: B 111 TYR cc_start: 0.8168 (m-80) cc_final: 0.7756 (m-80) REVERT: B 245 SER cc_start: 0.8955 (p) cc_final: 0.8650 (p) REVERT: B 297 TRP cc_start: 0.8568 (m100) cc_final: 0.8192 (m100) REVERT: B 321 THR cc_start: 0.7736 (p) cc_final: 0.7507 (p) REVERT: G 29 LYS cc_start: 0.8886 (tptm) cc_final: 0.8612 (tptp) REVERT: N 33 LYS cc_start: 0.8597 (tttm) cc_final: 0.8065 (tmtt) REVERT: R 154 ILE cc_start: 0.8161 (tp) cc_final: 0.7792 (tp) REVERT: R 156 PHE cc_start: 0.7847 (m-80) cc_final: 0.7643 (m-80) outliers start: 39 outliers final: 28 residues processed: 261 average time/residue: 0.0937 time to fit residues: 33.3201 Evaluate side-chains 243 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 87 THR 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 269 ILE 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 73 VAL 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: 6.9990 chunk 90 optimal weight: 0.0770 chunk 81 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 293 ASN N 53 GLN ** R 41 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 = 0.4288 r_free = 0.4288 target = 0.206600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.170401 restraints weight = 9047.022| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.19 r_work: 0.3811 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8278 Z= 0.151 Angle : 0.605 11.006 11236 Z= 0.303 Chirality : 0.042 0.164 1279 Planarity : 0.004 0.045 1418 Dihedral : 5.181 59.223 1133 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.81 % Allowed : 21.74 % Favored : 72.44 % 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: 0.69 (0.26), residues: 395 sheet: -2.34 (0.33), residues: 204 loop : -1.18 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 214 TYR 0.012 0.001 TYR N 115 PHE 0.009 0.001 PHE B 241 TRP 0.014 0.002 TRP A 281 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 8274) covalent geometry : angle 0.59384 / 0.30 (11228) SS BOND : bond 0.01011 / 0.48 ( 4) SS BOND : angle 4.29526 / 2.49 ( 8) hydrogen bonds : bond 0.03841 / 2.57 ( 410) hydrogen bonds : angle 5.24510 / 3.67 ( 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 271 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5410 (t80) cc_final: 0.4488 (t80) REVERT: A 292 ASN cc_start: 0.7956 (t0) cc_final: 0.7635 (t0) REVERT: A 295 ASP cc_start: 0.7210 (p0) cc_final: 0.6798 (p0) REVERT: B 111 TYR cc_start: 0.8156 (m-80) cc_final: 0.7777 (m-80) REVERT: B 152 LEU cc_start: 0.7649 (mt) cc_final: 0.7284 (mt) REVERT: B 168 LEU cc_start: 0.8501 (tp) cc_final: 0.8241 (tp) REVERT: B 321 THR cc_start: 0.7893 (p) cc_final: 0.7660 (p) REVERT: B 334 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.8022 (t) REVERT: N 33 LYS cc_start: 0.8478 (tttm) cc_final: 0.7838 (tmtt) REVERT: R 154 ILE cc_start: 0.8164 (tp) cc_final: 0.7804 (tp) REVERT: R 156 PHE cc_start: 0.7797 (m-80) cc_final: 0.7574 (m-80) outliers start: 50 outliers final: 32 residues processed: 258 average time/residue: 0.0872 time to fit residues: 30.9018 Evaluate side-chains 241 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 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 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 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 327 VAL Chi-restraints excluded: chain B residue 334 SER 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 73 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 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 = 0.4278 r_free = 0.4278 target = 0.205774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.169986 restraints weight = 9018.490| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.19 r_work: 0.3817 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8278 Z= 0.154 Angle : 0.606 10.429 11236 Z= 0.304 Chirality : 0.043 0.159 1279 Planarity : 0.004 0.056 1418 Dihedral : 5.245 59.081 1133 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.88 % Allowed : 23.02 % Favored : 72.09 % 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: -1.04 (0.27), residues: 1015 helix: 0.69 (0.26), residues: 400 sheet: -2.15 (0.33), residues: 210 loop : -1.13 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 214 TYR 0.013 0.001 TYR R 331 PHE 0.021 0.001 PHE B 292 TRP 0.013 0.002 TRP A 281 HIS 0.007 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 8274) covalent geometry : angle 0.60022 / 0.30 (11228) SS BOND : bond 0.00321 / 0.17 ( 4) SS BOND : angle 3.23081 / 1.85 ( 8) hydrogen bonds : bond 0.03809 / 2.55 ( 410) hydrogen bonds : angle 5.22745 / 3.65 ( 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 255 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5413 (t80) cc_final: 0.4502 (t80) REVERT: A 292 ASN cc_start: 0.7976 (t0) cc_final: 0.7701 (t0) REVERT: B 111 TYR cc_start: 0.8176 (m-80) cc_final: 0.7751 (m-80) REVERT: B 152 LEU cc_start: 0.7645 (mt) cc_final: 0.7269 (mt) REVERT: B 168 LEU cc_start: 0.8481 (tp) cc_final: 0.8250 (tp) REVERT: B 321 THR cc_start: 0.7919 (p) cc_final: 0.7680 (p) REVERT: B 334 SER cc_start: 0.8431 (OUTLIER) cc_final: 0.8216 (p) REVERT: G 29 LYS cc_start: 0.8721 (tptp) cc_final: 0.8289 (tptt) REVERT: N 33 LYS cc_start: 0.8459 (tttm) cc_final: 0.7784 (tmtt) REVERT: R 154 ILE cc_start: 0.8138 (tp) cc_final: 0.7786 (tp) REVERT: R 156 PHE cc_start: 0.7729 (m-80) cc_final: 0.7523 (m-80) outliers start: 42 outliers final: 31 residues processed: 241 average time/residue: 0.0808 time to fit residues: 27.0810 Evaluate side-chains 240 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 A residue 335 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 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 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 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 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 73 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 35 ASN N 39 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.208350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.172481 restraints weight = 9095.521| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.19 r_work: 0.3815 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8278 Z= 0.157 Angle : 0.606 11.360 11236 Z= 0.304 Chirality : 0.042 0.158 1279 Planarity : 0.005 0.061 1418 Dihedral : 5.303 56.695 1133 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.12 % Allowed : 24.53 % 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: -0.98 (0.27), residues: 1015 helix: 0.73 (0.26), residues: 400 sheet: -2.11 (0.33), residues: 210 loop : -1.09 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 342 TYR 0.009 0.001 TYR N 115 PHE 0.022 0.001 PHE B 292 TRP 0.014 0.002 TRP A 281 HIS 0.007 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 8274) covalent geometry : angle 0.60126 / 0.30 (11228) SS BOND : bond 0.00489 / 0.25 ( 4) SS BOND : angle 2.96247 / 1.43 ( 8) hydrogen bonds : bond 0.03746 / 2.51 ( 410) hydrogen bonds : angle 5.20437 / 3.63 ( 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 256 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5492 (t80) cc_final: 0.4613 (t80) REVERT: A 292 ASN cc_start: 0.8029 (t0) cc_final: 0.7735 (t0) REVERT: A 295 ASP cc_start: 0.7143 (p0) cc_final: 0.6752 (p0) REVERT: A 381 ASP cc_start: 0.8350 (m-30) cc_final: 0.8077 (t0) REVERT: B 111 TYR cc_start: 0.8159 (m-80) cc_final: 0.7765 (m-80) REVERT: B 152 LEU cc_start: 0.7720 (mt) cc_final: 0.7318 (mt) REVERT: B 297 TRP cc_start: 0.8589 (m100) cc_final: 0.8367 (m100) REVERT: B 321 THR cc_start: 0.7933 (p) cc_final: 0.7692 (p) REVERT: G 29 LYS cc_start: 0.8672 (tptp) cc_final: 0.8219 (tptt) REVERT: N 33 LYS cc_start: 0.8626 (tttm) cc_final: 0.7942 (tmtt) REVERT: R 123 TRP cc_start: 0.7695 (m100) cc_final: 0.7212 (m100) REVERT: R 154 ILE cc_start: 0.8115 (tp) cc_final: 0.7881 (tp) REVERT: R 156 PHE cc_start: 0.7722 (m-80) cc_final: 0.7502 (m-80) outliers start: 44 outliers final: 28 residues processed: 245 average time/residue: 0.0853 time to fit residues: 29.0782 Evaluate side-chains 230 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 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 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 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 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 73 VAL 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: 0.9980 chunk 47 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 35 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.208972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.173433 restraints weight = 9012.956| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.19 r_work: 0.3825 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8278 Z= 0.150 Angle : 0.614 11.305 11236 Z= 0.306 Chirality : 0.043 0.148 1279 Planarity : 0.004 0.045 1418 Dihedral : 5.051 58.107 1132 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.07 % Allowed : 25.70 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.27), residues: 1015 helix: 0.76 (0.26), residues: 399 sheet: -2.11 (0.33), residues: 211 loop : -0.98 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 342 TYR 0.013 0.001 TYR B 264 PHE 0.021 0.001 PHE B 292 TRP 0.013 0.002 TRP A 281 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 8274) covalent geometry : angle 0.61069 / 0.30 (11228) SS BOND : bond 0.00299 / 0.15 ( 4) SS BOND : angle 2.49750 / 1.27 ( 8) hydrogen bonds : bond 0.03647 / 2.44 ( 410) hydrogen bonds : angle 5.16076 / 3.59 ( 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 242 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5567 (t80) cc_final: 0.4673 (t80) REVERT: A 292 ASN cc_start: 0.8019 (t0) cc_final: 0.7771 (t0) REVERT: A 389 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7958 (tpp-160) REVERT: B 111 TYR cc_start: 0.8150 (m-80) cc_final: 0.7706 (m-80) REVERT: B 297 TRP cc_start: 0.8571 (m100) cc_final: 0.8352 (m100) REVERT: B 321 THR cc_start: 0.7934 (p) cc_final: 0.7685 (p) REVERT: G 29 LYS cc_start: 0.8655 (tptp) cc_final: 0.8216 (tptt) REVERT: N 33 LYS cc_start: 0.8602 (tttm) cc_final: 0.7932 (tmtt) REVERT: R 32 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7748 (tt) REVERT: R 81 LYS cc_start: 0.8423 (tppt) cc_final: 0.8171 (tppt) REVERT: R 154 ILE cc_start: 0.8038 (tp) cc_final: 0.7807 (tp) REVERT: R 156 PHE cc_start: 0.7738 (m-10) cc_final: 0.7518 (m-80) outliers start: 35 outliers final: 29 residues processed: 232 average time/residue: 0.0827 time to fit residues: 26.5991 Evaluate side-chains 231 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 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 286 SER Chi-restraints excluded: chain A residue 335 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 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 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 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 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: 0.9980 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 266 HIS B 293 ASN N 35 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.206586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.170471 restraints weight = 8967.159| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.18 r_work: 0.3794 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8278 Z= 0.175 Angle : 0.625 10.648 11236 Z= 0.313 Chirality : 0.043 0.153 1279 Planarity : 0.004 0.051 1418 Dihedral : 5.043 56.373 1132 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.19 % Allowed : 26.51 % Favored : 69.30 % 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: -0.97 (0.27), residues: 1015 helix: 0.67 (0.26), residues: 400 sheet: -2.19 (0.33), residues: 213 loop : -0.94 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 342 TYR 0.017 0.002 TYR R 218 PHE 0.022 0.001 PHE B 292 TRP 0.033 0.002 TRP B 99 HIS 0.007 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 8274) covalent geometry : angle 0.62235 / 0.31 (11228) SS BOND : bond 0.00285 / 0.15 ( 4) SS BOND : angle 2.39328 / 1.27 ( 8) hydrogen bonds : bond 0.03745 / 2.50 ( 410) hydrogen bonds : angle 5.22876 / 3.62 ( 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 242 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 ASN cc_start: 0.8061 (t0) cc_final: 0.7819 (t0) REVERT: B 111 TYR cc_start: 0.8211 (m-80) cc_final: 0.7761 (m-80) REVERT: B 152 LEU cc_start: 0.7984 (mt) cc_final: 0.7747 (mt) REVERT: G 29 LYS cc_start: 0.8657 (tptp) cc_final: 0.8264 (tptt) REVERT: N 33 LYS cc_start: 0.8631 (tttm) cc_final: 0.7926 (tmtt) REVERT: R 32 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7765 (tt) REVERT: R 60 ASN cc_start: 0.8076 (m-40) cc_final: 0.7782 (m-40) REVERT: R 123 TRP cc_start: 0.7711 (m100) cc_final: 0.7241 (m100) REVERT: R 154 ILE cc_start: 0.8082 (tp) cc_final: 0.7847 (tp) REVERT: R 156 PHE cc_start: 0.7869 (m-10) cc_final: 0.7639 (m-80) outliers start: 36 outliers final: 26 residues processed: 232 average time/residue: 0.0859 time to fit residues: 27.3234 Evaluate side-chains 226 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 A residue 335 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 0.0270 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 35 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.210967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.175602 restraints weight = 9076.705| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.20 r_work: 0.3848 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3735 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= 0.138 Angle : 0.621 12.495 11236 Z= 0.310 Chirality : 0.043 0.177 1279 Planarity : 0.004 0.041 1418 Dihedral : 4.975 48.137 1132 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.72 % Allowed : 26.05 % Favored : 70.23 % 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: -0.89 (0.27), residues: 1015 helix: 0.73 (0.26), residues: 400 sheet: -2.15 (0.33), residues: 205 loop : -0.94 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 342 TYR 0.013 0.002 TYR B 264 PHE 0.020 0.001 PHE B 292 TRP 0.031 0.002 TRP B 99 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 8274) covalent geometry : angle 0.61891 / 0.31 (11228) SS BOND : bond 0.00182 / 0.09 ( 4) SS BOND : angle 2.05236 / 1.07 ( 8) hydrogen bonds : bond 0.03584 / 2.40 ( 410) hydrogen bonds : angle 5.18100 / 3.59 ( 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 235 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ASN cc_start: 0.7997 (t0) cc_final: 0.7758 (t0) REVERT: A 389 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7930 (tpp-160) REVERT: B 111 TYR cc_start: 0.8144 (m-80) cc_final: 0.7676 (m-80) REVERT: B 152 LEU cc_start: 0.7907 (mt) cc_final: 0.7650 (mt) REVERT: B 297 TRP cc_start: 0.8524 (m100) cc_final: 0.8267 (m100) REVERT: G 29 LYS cc_start: 0.8641 (tptp) cc_final: 0.8277 (tptt) REVERT: N 33 LYS cc_start: 0.8626 (tttm) cc_final: 0.7945 (tmtt) REVERT: R 32 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7740 (tt) REVERT: R 123 TRP cc_start: 0.7642 (m100) cc_final: 0.7203 (m100) REVERT: R 154 ILE cc_start: 0.8045 (tp) cc_final: 0.7815 (tp) REVERT: R 156 PHE cc_start: 0.7779 (m-10) cc_final: 0.7496 (m-80) outliers start: 32 outliers final: 27 residues processed: 226 average time/residue: 0.0866 time to fit residues: 27.1433 Evaluate side-chains 226 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 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 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 227 SER Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 61 optimal weight: 0.0050 chunk 46 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 overall best weight: 0.6974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN A 292 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** R 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.209408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.173906 restraints weight = 9012.558| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.20 r_work: 0.3833 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8278 Z= 0.152 Angle : 0.628 11.953 11236 Z= 0.314 Chirality : 0.043 0.174 1279 Planarity : 0.004 0.042 1418 Dihedral : 4.855 44.888 1132 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.49 % Allowed : 26.28 % Favored : 70.23 % 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: -0.84 (0.27), residues: 1015 helix: 0.74 (0.26), residues: 399 sheet: -2.07 (0.33), residues: 211 loop : -0.87 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 342 TYR 0.015 0.002 TYR N 115 PHE 0.020 0.001 PHE B 292 TRP 0.031 0.002 TRP B 99 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 8274) covalent geometry : angle 0.62617 / 0.31 (11228) SS BOND : bond 0.00194 / 0.10 ( 4) SS BOND : angle 2.05173 / 1.10 ( 8) hydrogen bonds : bond 0.03588 / 2.39 ( 410) hydrogen bonds : angle 5.18849 / 3.59 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2021.92 seconds wall clock time: 35 minutes 32.77 seconds (2132.77 seconds total)