Starting phenix.real_space_refine on Fri Aug 22 21:04:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tyw_41729/08_2025/8tyw_41729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tyw_41729/08_2025/8tyw_41729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tyw_41729/08_2025/8tyw_41729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tyw_41729/08_2025/8tyw_41729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tyw_41729/08_2025/8tyw_41729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tyw_41729/08_2025/8tyw_41729.map" } resolution = 3.43 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5022 2.51 5 N 1386 2.21 5 O 1483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7938 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2012 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2593 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1938 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 437 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 958 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 1.88, per 1000 atoms: 0.24 Number of scatterers: 7938 At special positions: 0 Unit cell: (75.712, 104.832, 128.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1483 8.00 N 1386 7.00 C 5022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 209 " - pdb=" SG CYS A 216 " distance=2.03 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 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: 0.69 Conformation dependent library (CDL) restraints added in 395.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 10 sheets defined 41.9% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 73 through 100 removed outlier: 3.807A pdb=" N VAL A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 135 removed outlier: 3.861A pdb=" N TYR A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 172 Processing helix chain 'A' and resid 173 through 176 removed outlier: 3.541A pdb=" N TYR A 176 " --> pdb=" O ALA A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 176' Processing helix chain 'A' and resid 178 through 206 removed outlier: 4.477A pdb=" N GLY A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 3.520A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 263 removed outlier: 3.995A pdb=" N VAL A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 302 removed outlier: 4.591A pdb=" N THR A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TRP A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Proline residue: A 294 - end of helix Processing helix chain 'A' and resid 307 through 330 removed outlier: 4.314A pdb=" N THR A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Proline residue: A 317 - end of helix Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 333 through 344 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.654A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.645A pdb=" N GLN B 32 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 39 removed outlier: 3.939A pdb=" N GLN C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 64 Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.548A pdb=" N CYS C 237 " --> pdb=" O TRP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 removed outlier: 4.032A pdb=" N ALA C 268 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.524A pdb=" N GLU C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 316 Proline residue: C 313 - end of helix removed outlier: 3.662A pdb=" N ALA C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 353 removed outlier: 3.892A pdb=" N ILE C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 391 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.629A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.539A pdb=" N ASP N 90 " --> pdb=" O LYS N 87 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52 removed outlier: 4.083A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.669A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.464A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.561A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.657A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.742A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.969A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 207 through 214 removed outlier: 3.920A pdb=" N ASP C 223 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C 210 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET C 221 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N HIS C 41 " --> pdb=" O HIS C 220 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE C 222 " --> pdb=" O HIS C 41 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 43 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N VAL C 224 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LEU C 45 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG C 42 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE C 245 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU C 44 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL C 247 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU C 46 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ALA C 249 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL C 287 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N HIS C 362 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU C 289 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.932A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.601A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1164 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: 1.11 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2601 1.34 - 1.46: 1430 1.46 - 1.57: 4000 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 8096 Sorted by residual: bond pdb=" CA THR B 50 " pdb=" CB THR B 50 " ideal model delta sigma weight residual 1.528 1.569 -0.041 1.51e-02 4.39e+03 7.35e+00 bond pdb=" CG LEU C 346 " pdb=" CD2 LEU C 346 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.24e+00 bond pdb=" CB LYS C 271 " pdb=" CG LYS C 271 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.73e+00 bond pdb=" CD LYS C 271 " pdb=" CE LYS C 271 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.42e+00 bond pdb=" CB ASN A 321 " pdb=" CG ASN A 321 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.37e+00 ... (remaining 8091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 10733 2.67 - 5.33: 209 5.33 - 8.00: 41 8.00 - 10.67: 12 10.67 - 13.34: 2 Bond angle restraints: 10997 Sorted by residual: angle pdb=" CB LYS C 271 " pdb=" CG LYS C 271 " pdb=" CD LYS C 271 " ideal model delta sigma weight residual 111.30 97.96 13.34 2.30e+00 1.89e-01 3.36e+01 angle pdb=" CB ARG A 179 " pdb=" CG ARG A 179 " pdb=" CD ARG A 179 " ideal model delta sigma weight residual 111.30 121.33 -10.03 2.30e+00 1.89e-01 1.90e+01 angle pdb=" CA ILE A 86 " pdb=" CB ILE A 86 " pdb=" CG1 ILE A 86 " ideal model delta sigma weight residual 110.40 117.81 -7.41 1.70e+00 3.46e-01 1.90e+01 angle pdb=" CA GLU G 22 " pdb=" CB GLU G 22 " pdb=" CG GLU G 22 " ideal model delta sigma weight residual 114.10 122.81 -8.71 2.00e+00 2.50e-01 1.90e+01 angle pdb=" CG ARG G 13 " pdb=" CD ARG G 13 " pdb=" NE ARG G 13 " ideal model delta sigma weight residual 112.00 121.27 -9.27 2.20e+00 2.07e-01 1.78e+01 ... (remaining 10992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 4024 17.37 - 34.74: 558 34.74 - 52.11: 175 52.11 - 69.48: 34 69.48 - 86.85: 12 Dihedral angle restraints: 4803 sinusoidal: 1827 harmonic: 2976 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 157.76 -64.76 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CA ASN A 172 " pdb=" C ASN A 172 " pdb=" N ALA A 173 " pdb=" CA ALA A 173 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLN A 132 " pdb=" C GLN A 132 " pdb=" N TYR A 133 " pdb=" CA TYR A 133 " ideal model delta harmonic sigma weight residual 180.00 159.96 20.04 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 4800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1069 0.072 - 0.144: 173 0.144 - 0.217: 18 0.217 - 0.289: 2 0.289 - 0.361: 3 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CB VAL A 283 " pdb=" CA VAL A 283 " pdb=" CG1 VAL A 283 " pdb=" CG2 VAL A 283 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CB THR A 192 " pdb=" CA THR A 192 " pdb=" OG1 THR A 192 " pdb=" CG2 THR A 192 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CG LEU A 281 " pdb=" CB LEU A 281 " pdb=" CD1 LEU A 281 " pdb=" CD2 LEU A 281 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1262 not shown) Planarity restraints: 1405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 362 " 0.023 2.00e-02 2.50e+03 2.41e-02 8.72e+00 pdb=" CG HIS C 362 " -0.051 2.00e-02 2.50e+03 pdb=" ND1 HIS C 362 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS C 362 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 HIS C 362 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS C 362 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 105 " -0.047 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO A 106 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 68 " 0.190 9.50e-02 1.11e+02 8.57e-02 5.60e+00 pdb=" NE ARG B 68 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 68 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 68 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 68 " 0.001 2.00e-02 2.50e+03 ... (remaining 1402 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2448 2.82 - 3.34: 7113 3.34 - 3.86: 13388 3.86 - 4.38: 14455 4.38 - 4.90: 25591 Nonbonded interactions: 62995 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.297 3.040 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.309 3.040 nonbonded pdb=" OG SER N 112 " pdb=" O THR N 114 " model vdw 2.319 3.040 nonbonded pdb=" NZ LYS B 78 " pdb=" OD2 ASP C 33 " model vdw 2.331 3.120 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.337 3.040 ... (remaining 62990 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.430 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.005 0.068 8099 Z= 0.217 Angle : 0.932 13.336 11003 Z= 0.484 Chirality : 0.055 0.361 1265 Planarity : 0.007 0.086 1405 Dihedral : 18.203 86.850 2870 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.59 % Allowed : 37.75 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -1.15 (0.24), residues: 1008 helix: -0.24 (0.22), residues: 401 sheet: -0.09 (0.38), residues: 207 loop : -1.57 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG G 13 TYR 0.011 0.002 TYR B 289 PHE 0.029 0.002 PHE C 212 TRP 0.016 0.002 TRP C 234 HIS 0.025 0.002 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 8096) covalent geometry : angle 0.93149 (10997) SS BOND : bond 0.00137 ( 3) SS BOND : angle 1.16030 ( 6) hydrogen bonds : bond 0.15946 ( 401) hydrogen bonds : angle 6.73295 ( 1164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 274 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8423 (m-10) cc_final: 0.8132 (m-80) REVERT: A 179 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.7479 (tpp-160) REVERT: A 281 LEU cc_start: 0.8104 (tp) cc_final: 0.7789 (mm) REVERT: B 22 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.8047 (ttm-80) REVERT: B 258 ASP cc_start: 0.7576 (t0) cc_final: 0.7163 (t0) REVERT: B 278 PHE cc_start: 0.8697 (m-80) cc_final: 0.8279 (m-80) REVERT: C 273 PHE cc_start: 0.8151 (t80) cc_final: 0.7806 (t80) REVERT: G 13 ARG cc_start: 0.8220 (mtm110) cc_final: 0.7720 (ptt-90) outliers start: 5 outliers final: 2 residues processed: 275 average time/residue: 0.1247 time to fit residues: 42.6375 Evaluate side-chains 271 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 269 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain C residue 33 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.0020 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 ASN C 267 GLN C 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.127834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110707 restraints weight = 13052.689| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.76 r_work: 0.3279 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8099 Z= 0.140 Angle : 0.562 6.748 11003 Z= 0.297 Chirality : 0.042 0.176 1265 Planarity : 0.004 0.061 1405 Dihedral : 4.534 39.574 1116 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.33 % Allowed : 31.83 % Favored : 62.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 0.02 (0.26), residues: 1008 helix: 1.33 (0.25), residues: 402 sheet: 0.04 (0.37), residues: 212 loop : -1.40 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.009 0.001 TYR N 95 PHE 0.010 0.001 PHE C 222 TRP 0.012 0.001 TRP C 234 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8096) covalent geometry : angle 0.56154 (10997) SS BOND : bond 0.00125 ( 3) SS BOND : angle 0.74822 ( 6) hydrogen bonds : bond 0.03721 ( 401) hydrogen bonds : angle 4.65874 ( 1164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 283 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.7792 (tpp-160) cc_final: 0.7467 (tpp-160) REVERT: A 246 VAL cc_start: 0.8511 (t) cc_final: 0.8215 (p) REVERT: B 22 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.7993 (ttm-80) REVERT: B 136 SER cc_start: 0.8499 (p) cc_final: 0.8152 (m) REVERT: B 142 HIS cc_start: 0.6617 (OUTLIER) cc_final: 0.6115 (p90) REVERT: B 163 ASP cc_start: 0.7940 (p0) cc_final: 0.7548 (p0) REVERT: B 186 ASP cc_start: 0.7864 (p0) cc_final: 0.7616 (p0) REVERT: B 219 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7476 (mmt90) REVERT: B 261 LEU cc_start: 0.8456 (mt) cc_final: 0.8234 (mp) REVERT: B 294 CYS cc_start: 0.8182 (p) cc_final: 0.7869 (p) REVERT: B 298 ASP cc_start: 0.7472 (t70) cc_final: 0.7106 (t0) REVERT: B 331 SER cc_start: 0.8372 (t) cc_final: 0.8096 (p) REVERT: C 12 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7521 (pm20) REVERT: C 23 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8503 (t0) REVERT: C 210 THR cc_start: 0.8021 (OUTLIER) cc_final: 0.7806 (p) REVERT: C 230 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7083 (mt-10) REVERT: C 233 LYS cc_start: 0.8299 (mtpp) cc_final: 0.8013 (mtpp) REVERT: C 273 PHE cc_start: 0.8204 (t80) cc_final: 0.7905 (t80) REVERT: G 14 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8673 (pttm) outliers start: 45 outliers final: 24 residues processed: 308 average time/residue: 0.1139 time to fit residues: 44.1036 Evaluate side-chains 306 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.123595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106669 restraints weight = 13063.031| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.70 r_work: 0.3188 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8099 Z= 0.269 Angle : 0.638 7.547 11003 Z= 0.335 Chirality : 0.047 0.208 1265 Planarity : 0.004 0.052 1405 Dihedral : 4.757 39.891 1114 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.86 % Allowed : 31.01 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 0.17 (0.26), residues: 1008 helix: 1.60 (0.25), residues: 396 sheet: -0.11 (0.36), residues: 218 loop : -1.28 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 68 TYR 0.016 0.002 TYR N 95 PHE 0.013 0.002 PHE C 363 TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 8096) covalent geometry : angle 0.63727 (10997) SS BOND : bond 0.00454 ( 3) SS BOND : angle 1.57808 ( 6) hydrogen bonds : bond 0.04295 ( 401) hydrogen bonds : angle 4.62895 ( 1164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 274 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.8162 (mp) cc_final: 0.7914 (mp) REVERT: A 118 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6500 (t0) REVERT: A 137 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.7428 (p) REVERT: A 157 SER cc_start: 0.8631 (m) cc_final: 0.8219 (p) REVERT: A 179 ARG cc_start: 0.7761 (tpp-160) cc_final: 0.7515 (tpp-160) REVERT: A 246 VAL cc_start: 0.8508 (t) cc_final: 0.8272 (p) REVERT: B 17 GLN cc_start: 0.8614 (tp-100) cc_final: 0.8216 (tp-100) REVERT: B 22 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.7643 (mtm-85) REVERT: B 33 ILE cc_start: 0.9074 (tt) cc_final: 0.8786 (tp) REVERT: B 57 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8275 (ptpp) REVERT: B 100 VAL cc_start: 0.8512 (m) cc_final: 0.8271 (p) REVERT: B 136 SER cc_start: 0.8593 (p) cc_final: 0.8229 (m) REVERT: B 142 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.6301 (p90) REVERT: B 226 GLU cc_start: 0.7565 (pt0) cc_final: 0.7241 (pt0) REVERT: B 258 ASP cc_start: 0.7708 (t0) cc_final: 0.7066 (t0) REVERT: B 289 TYR cc_start: 0.8189 (m-80) cc_final: 0.7735 (m-80) REVERT: B 298 ASP cc_start: 0.7507 (t70) cc_final: 0.6998 (t0) REVERT: C 210 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7966 (p) REVERT: C 273 PHE cc_start: 0.8320 (t80) cc_final: 0.7902 (t80) REVERT: G 14 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8666 (pttm) REVERT: N 72 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7450 (ttm-80) outliers start: 58 outliers final: 36 residues processed: 308 average time/residue: 0.1341 time to fit residues: 51.2391 Evaluate side-chains 314 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** C 362 HIS ** 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 = 0.3614 r_free = 0.3614 target = 0.123392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.106367 restraints weight = 13365.559| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.72 r_work: 0.3170 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8099 Z= 0.249 Angle : 0.629 9.008 11003 Z= 0.330 Chirality : 0.046 0.250 1265 Planarity : 0.004 0.050 1405 Dihedral : 4.714 36.027 1114 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 7.93 % Allowed : 30.53 % Favored : 61.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 0.32 (0.26), residues: 1008 helix: 1.68 (0.25), residues: 404 sheet: -0.18 (0.36), residues: 220 loop : -1.12 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 68 TYR 0.013 0.002 TYR N 95 PHE 0.015 0.002 PHE C 363 TRP 0.017 0.002 TRP B 169 HIS 0.015 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 8096) covalent geometry : angle 0.62177 (10997) SS BOND : bond 0.00185 ( 3) SS BOND : angle 4.11939 ( 6) hydrogen bonds : bond 0.04058 ( 401) hydrogen bonds : angle 4.47332 ( 1164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 279 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7948 (mp) REVERT: A 118 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6737 (t0) REVERT: A 120 LEU cc_start: 0.8393 (mt) cc_final: 0.7971 (tp) REVERT: A 137 SER cc_start: 0.7696 (OUTLIER) cc_final: 0.7298 (p) REVERT: A 157 SER cc_start: 0.8655 (m) cc_final: 0.8213 (p) REVERT: A 179 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.7418 (tpp-160) REVERT: A 183 LEU cc_start: 0.8712 (tt) cc_final: 0.8347 (tp) REVERT: A 246 VAL cc_start: 0.8503 (t) cc_final: 0.8269 (p) REVERT: B 17 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8227 (tp-100) REVERT: B 22 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.7701 (ttm-80) REVERT: B 57 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8289 (ptpp) REVERT: B 100 VAL cc_start: 0.8556 (m) cc_final: 0.8277 (p) REVERT: B 136 SER cc_start: 0.8549 (p) cc_final: 0.8125 (m) REVERT: B 142 HIS cc_start: 0.7000 (OUTLIER) cc_final: 0.6371 (p90) REVERT: B 161 SER cc_start: 0.8415 (m) cc_final: 0.7872 (p) REVERT: B 175 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7739 (mm-40) REVERT: B 219 ARG cc_start: 0.7797 (mmt90) cc_final: 0.7450 (mmt90) REVERT: B 226 GLU cc_start: 0.7498 (pt0) cc_final: 0.7079 (pt0) REVERT: B 258 ASP cc_start: 0.7679 (t0) cc_final: 0.7058 (t0) REVERT: B 283 ARG cc_start: 0.8172 (tpt-90) cc_final: 0.7828 (tpt-90) REVERT: B 289 TYR cc_start: 0.8244 (m-80) cc_final: 0.7653 (m-80) REVERT: B 298 ASP cc_start: 0.7532 (t70) cc_final: 0.6839 (t0) REVERT: B 317 CYS cc_start: 0.7912 (p) cc_final: 0.7540 (p) REVERT: C 12 GLN cc_start: 0.8123 (pm20) cc_final: 0.7549 (pm20) REVERT: C 23 ASN cc_start: 0.8791 (t0) cc_final: 0.8551 (t0) REVERT: C 210 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7972 (p) REVERT: C 278 ASN cc_start: 0.8780 (m-40) cc_final: 0.8573 (m110) REVERT: C 362 HIS cc_start: 0.8273 (m170) cc_final: 0.8042 (m170) REVERT: C 392 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6893 (mm-30) REVERT: G 14 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8650 (pttm) REVERT: N 72 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7485 (ttm-80) outliers start: 67 outliers final: 40 residues processed: 320 average time/residue: 0.1307 time to fit residues: 52.2533 Evaluate side-chains 323 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 103 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN B 125 ASN ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107384 restraints weight = 13171.607| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.67 r_work: 0.3219 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8099 Z= 0.169 Angle : 0.581 7.241 11003 Z= 0.303 Chirality : 0.044 0.236 1265 Planarity : 0.004 0.049 1405 Dihedral : 4.465 32.611 1114 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 6.98 % Allowed : 32.19 % Favored : 60.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 0.54 (0.27), residues: 1008 helix: 1.91 (0.26), residues: 404 sheet: -0.14 (0.36), residues: 221 loop : -1.01 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.012 0.001 TYR N 95 PHE 0.009 0.001 PHE B 335 TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8096) covalent geometry : angle 0.57918 (10997) SS BOND : bond 0.00142 ( 3) SS BOND : angle 2.04678 ( 6) hydrogen bonds : bond 0.03690 ( 401) hydrogen bonds : angle 4.30959 ( 1164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 285 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.7227 (t0) cc_final: 0.6797 (p0) REVERT: A 86 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7830 (mp) REVERT: A 157 SER cc_start: 0.8633 (m) cc_final: 0.8157 (p) REVERT: A 179 ARG cc_start: 0.7763 (tpp-160) cc_final: 0.7440 (tpp-160) REVERT: A 183 LEU cc_start: 0.8743 (tt) cc_final: 0.8341 (tp) REVERT: A 246 VAL cc_start: 0.8495 (t) cc_final: 0.8220 (p) REVERT: B 17 GLN cc_start: 0.8596 (tp-100) cc_final: 0.8173 (tp-100) REVERT: B 22 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.7368 (mtm-85) REVERT: B 57 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8252 (ptpp) REVERT: B 100 VAL cc_start: 0.8479 (m) cc_final: 0.8223 (p) REVERT: B 136 SER cc_start: 0.8506 (p) cc_final: 0.8072 (m) REVERT: B 142 HIS cc_start: 0.6880 (OUTLIER) cc_final: 0.6418 (p90) REVERT: B 161 SER cc_start: 0.8447 (m) cc_final: 0.8068 (p) REVERT: B 226 GLU cc_start: 0.7575 (pt0) cc_final: 0.7109 (pt0) REVERT: B 258 ASP cc_start: 0.7667 (t0) cc_final: 0.6850 (t0) REVERT: B 260 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: B 283 ARG cc_start: 0.8177 (tpt-90) cc_final: 0.7793 (tpt-90) REVERT: B 289 TYR cc_start: 0.8224 (m-80) cc_final: 0.7588 (m-80) REVERT: B 298 ASP cc_start: 0.7528 (t70) cc_final: 0.6749 (t0) REVERT: C 23 ASN cc_start: 0.8802 (t0) cc_final: 0.8560 (t0) REVERT: C 210 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7857 (p) REVERT: C 232 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8445 (ttp-110) REVERT: C 273 PHE cc_start: 0.8330 (t80) cc_final: 0.7833 (t80) REVERT: C 278 ASN cc_start: 0.8845 (m-40) cc_final: 0.8625 (m110) REVERT: C 392 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6883 (mm-30) REVERT: G 13 ARG cc_start: 0.7973 (ptp-110) cc_final: 0.7540 (ptt-90) REVERT: G 14 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8678 (pttm) REVERT: N 72 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7562 (ttm-80) outliers start: 59 outliers final: 38 residues processed: 316 average time/residue: 0.1338 time to fit residues: 52.4286 Evaluate side-chains 326 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 103 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 86 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108714 restraints weight = 13138.431| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.67 r_work: 0.3243 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8099 Z= 0.120 Angle : 0.558 7.155 11003 Z= 0.290 Chirality : 0.043 0.205 1265 Planarity : 0.003 0.049 1405 Dihedral : 4.148 18.248 1112 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 7.22 % Allowed : 33.02 % Favored : 59.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 0.71 (0.27), residues: 1008 helix: 2.08 (0.26), residues: 403 sheet: -0.02 (0.36), residues: 220 loop : -0.98 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.011 0.001 TYR A 133 PHE 0.008 0.001 PHE A 131 TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8096) covalent geometry : angle 0.55729 (10997) SS BOND : bond 0.00115 ( 3) SS BOND : angle 1.50637 ( 6) hydrogen bonds : bond 0.03368 ( 401) hydrogen bonds : angle 4.17281 ( 1164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 284 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7789 (mp) REVERT: A 118 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6679 (t0) REVERT: A 157 SER cc_start: 0.8628 (m) cc_final: 0.8162 (p) REVERT: A 179 ARG cc_start: 0.7797 (tpp-160) cc_final: 0.7422 (tpp-160) REVERT: A 183 LEU cc_start: 0.8780 (tt) cc_final: 0.8163 (tp) REVERT: B 22 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.7455 (mtm-85) REVERT: B 57 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8056 (ptpp) REVERT: B 100 VAL cc_start: 0.8450 (m) cc_final: 0.8207 (p) REVERT: B 118 ASP cc_start: 0.7714 (p0) cc_final: 0.7339 (p0) REVERT: B 142 HIS cc_start: 0.6740 (OUTLIER) cc_final: 0.6334 (p90) REVERT: B 161 SER cc_start: 0.8458 (m) cc_final: 0.8163 (p) REVERT: B 226 GLU cc_start: 0.7580 (pt0) cc_final: 0.7136 (pt0) REVERT: B 258 ASP cc_start: 0.7654 (t0) cc_final: 0.6914 (t0) REVERT: B 260 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: B 283 ARG cc_start: 0.8170 (tpt-90) cc_final: 0.7773 (tpt-90) REVERT: B 289 TYR cc_start: 0.8207 (m-80) cc_final: 0.7603 (m-80) REVERT: B 298 ASP cc_start: 0.7375 (t70) cc_final: 0.6597 (t0) REVERT: B 314 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.8008 (mmm-85) REVERT: C 23 ASN cc_start: 0.8785 (t0) cc_final: 0.8545 (t0) REVERT: C 210 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7866 (p) REVERT: C 232 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8370 (ttp-110) REVERT: C 273 PHE cc_start: 0.8267 (t80) cc_final: 0.7872 (t80) REVERT: C 278 ASN cc_start: 0.8857 (m-40) cc_final: 0.8656 (m110) REVERT: C 392 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6863 (mm-30) REVERT: G 13 ARG cc_start: 0.7923 (ptp-110) cc_final: 0.7212 (ptp-110) REVERT: N 38 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8440 (ptt180) REVERT: N 72 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7603 (ttm-80) outliers start: 61 outliers final: 37 residues processed: 320 average time/residue: 0.1345 time to fit residues: 53.4866 Evaluate side-chains 325 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 280 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 103 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 29 optimal weight: 0.0040 chunk 24 optimal weight: 0.1980 chunk 73 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110959 restraints weight = 13037.977| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.59 r_work: 0.3278 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8099 Z= 0.126 Angle : 0.567 7.220 11003 Z= 0.296 Chirality : 0.043 0.199 1265 Planarity : 0.003 0.048 1405 Dihedral : 4.109 18.230 1112 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 6.75 % Allowed : 33.49 % Favored : 59.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 0.73 (0.27), residues: 1008 helix: 2.06 (0.26), residues: 404 sheet: 0.05 (0.37), residues: 212 loop : -0.95 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 68 TYR 0.011 0.001 TYR N 95 PHE 0.007 0.001 PHE B 199 TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8096) covalent geometry : angle 0.56585 (10997) SS BOND : bond 0.00106 ( 3) SS BOND : angle 1.82080 ( 6) hydrogen bonds : bond 0.03365 ( 401) hydrogen bonds : angle 4.14507 ( 1164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7765 (mp) REVERT: A 118 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6635 (t0) REVERT: A 119 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7150 (tp) REVERT: A 157 SER cc_start: 0.8641 (m) cc_final: 0.8175 (p) REVERT: A 179 ARG cc_start: 0.7763 (tpp-160) cc_final: 0.7437 (tpp-160) REVERT: A 183 LEU cc_start: 0.8815 (tt) cc_final: 0.8312 (tp) REVERT: A 246 VAL cc_start: 0.8514 (t) cc_final: 0.8294 (p) REVERT: B 17 GLN cc_start: 0.8530 (tp-100) cc_final: 0.8100 (tp-100) REVERT: B 22 ARG cc_start: 0.8361 (mtm-85) cc_final: 0.7408 (ttm110) REVERT: B 57 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8103 (ptpp) REVERT: B 100 VAL cc_start: 0.8440 (m) cc_final: 0.8192 (p) REVERT: B 118 ASP cc_start: 0.7676 (p0) cc_final: 0.7273 (p0) REVERT: B 142 HIS cc_start: 0.6722 (OUTLIER) cc_final: 0.6360 (p90) REVERT: B 149 CYS cc_start: 0.8056 (p) cc_final: 0.7815 (p) REVERT: B 219 ARG cc_start: 0.7654 (mmt90) cc_final: 0.7323 (mpt-90) REVERT: B 226 GLU cc_start: 0.7562 (pt0) cc_final: 0.7173 (pt0) REVERT: B 258 ASP cc_start: 0.7582 (t0) cc_final: 0.6998 (t0) REVERT: B 260 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: B 278 PHE cc_start: 0.8716 (m-80) cc_final: 0.8400 (m-80) REVERT: B 283 ARG cc_start: 0.8158 (tpt-90) cc_final: 0.7791 (tpt-90) REVERT: B 289 TYR cc_start: 0.8206 (m-80) cc_final: 0.7624 (m-80) REVERT: B 298 ASP cc_start: 0.7439 (t70) cc_final: 0.6668 (t0) REVERT: B 331 SER cc_start: 0.8525 (t) cc_final: 0.8228 (t) REVERT: C 23 ASN cc_start: 0.8769 (t0) cc_final: 0.8529 (t0) REVERT: C 210 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7855 (p) REVERT: C 232 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8378 (ttp-110) REVERT: C 273 PHE cc_start: 0.8210 (t80) cc_final: 0.7943 (t80) REVERT: C 392 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6858 (mm-30) REVERT: G 13 ARG cc_start: 0.7937 (ptp-110) cc_final: 0.7213 (ptp-110) REVERT: N 38 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8387 (ptt180) REVERT: N 72 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7597 (ttm-80) outliers start: 57 outliers final: 33 residues processed: 311 average time/residue: 0.1324 time to fit residues: 51.4024 Evaluate side-chains 320 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 277 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 103 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108876 restraints weight = 13055.496| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.59 r_work: 0.3275 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8099 Z= 0.165 Angle : 0.593 7.926 11003 Z= 0.309 Chirality : 0.044 0.208 1265 Planarity : 0.003 0.047 1405 Dihedral : 4.199 18.400 1112 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 7.22 % Allowed : 33.61 % Favored : 59.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 0.68 (0.27), residues: 1008 helix: 2.00 (0.26), residues: 404 sheet: 0.03 (0.37), residues: 212 loop : -0.95 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 68 TYR 0.012 0.001 TYR N 95 PHE 0.008 0.001 PHE C 290 TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8096) covalent geometry : angle 0.59275 (10997) SS BOND : bond 0.00086 ( 3) SS BOND : angle 1.00959 ( 6) hydrogen bonds : bond 0.03567 ( 401) hydrogen bonds : angle 4.20081 ( 1164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 292 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7826 (mp) REVERT: A 118 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6607 (t0) REVERT: A 119 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7174 (tp) REVERT: A 157 SER cc_start: 0.8660 (m) cc_final: 0.8191 (p) REVERT: A 179 ARG cc_start: 0.7778 (tpp-160) cc_final: 0.7443 (tpp-160) REVERT: A 183 LEU cc_start: 0.8840 (tt) cc_final: 0.8231 (tp) REVERT: A 246 VAL cc_start: 0.8522 (t) cc_final: 0.8300 (p) REVERT: B 22 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.7125 (ttm-80) REVERT: B 52 ARG cc_start: 0.7027 (mtm180) cc_final: 0.6714 (mtm180) REVERT: B 57 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8264 (ptpp) REVERT: B 100 VAL cc_start: 0.8447 (m) cc_final: 0.8220 (p) REVERT: B 118 ASP cc_start: 0.7693 (p0) cc_final: 0.7273 (p0) REVERT: B 142 HIS cc_start: 0.6958 (OUTLIER) cc_final: 0.6629 (p90) REVERT: B 219 ARG cc_start: 0.7685 (mmt90) cc_final: 0.7344 (mpt-90) REVERT: B 226 GLU cc_start: 0.7547 (pt0) cc_final: 0.7107 (pt0) REVERT: B 258 ASP cc_start: 0.7596 (t0) cc_final: 0.6597 (t0) REVERT: B 260 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: B 283 ARG cc_start: 0.8229 (tpt-90) cc_final: 0.7800 (tpt-90) REVERT: B 289 TYR cc_start: 0.8226 (m-80) cc_final: 0.7627 (m-80) REVERT: B 298 ASP cc_start: 0.7474 (t70) cc_final: 0.6705 (t0) REVERT: C 23 ASN cc_start: 0.8786 (t0) cc_final: 0.8551 (t0) REVERT: C 210 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7896 (p) REVERT: C 273 PHE cc_start: 0.8214 (t80) cc_final: 0.7948 (t80) REVERT: C 299 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: C 392 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6866 (mm-30) REVERT: G 13 ARG cc_start: 0.7964 (ptp-110) cc_final: 0.7271 (ptp-110) REVERT: N 38 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8487 (ptt180) REVERT: N 72 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7504 (ttm-80) outliers start: 61 outliers final: 39 residues processed: 325 average time/residue: 0.1254 time to fit residues: 51.0685 Evaluate side-chains 340 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 291 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 103 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS C 267 GLN ** C 362 HIS ** 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 = 0.3665 r_free = 0.3665 target = 0.126706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110075 restraints weight = 13043.077| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.59 r_work: 0.3272 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8099 Z= 0.159 Angle : 0.605 7.766 11003 Z= 0.315 Chirality : 0.044 0.213 1265 Planarity : 0.003 0.047 1405 Dihedral : 4.237 18.300 1112 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 6.86 % Allowed : 33.73 % Favored : 59.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 0.68 (0.27), residues: 1008 helix: 2.00 (0.26), residues: 404 sheet: 0.01 (0.37), residues: 212 loop : -0.93 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 232 TYR 0.013 0.001 TYR N 95 PHE 0.008 0.001 PHE B 199 TRP 0.014 0.002 TRP B 211 HIS 0.006 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8096) covalent geometry : angle 0.60398 (10997) SS BOND : bond 0.00089 ( 3) SS BOND : angle 1.68275 ( 6) hydrogen bonds : bond 0.03547 ( 401) hydrogen bonds : angle 4.16558 ( 1164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 280 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7782 (mp) REVERT: A 118 ASP cc_start: 0.7007 (OUTLIER) cc_final: 0.6637 (t0) REVERT: A 119 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7179 (tp) REVERT: A 157 SER cc_start: 0.8656 (m) cc_final: 0.8189 (p) REVERT: A 179 ARG cc_start: 0.7812 (tpp-160) cc_final: 0.7474 (tpp-160) REVERT: A 183 LEU cc_start: 0.8845 (tt) cc_final: 0.8227 (tp) REVERT: A 246 VAL cc_start: 0.8520 (t) cc_final: 0.8300 (p) REVERT: B 9 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7215 (pp30) REVERT: B 22 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.7335 (mtm-85) REVERT: B 52 ARG cc_start: 0.7056 (mtm180) cc_final: 0.6760 (mtm180) REVERT: B 57 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8232 (ptpp) REVERT: B 100 VAL cc_start: 0.8451 (m) cc_final: 0.8212 (p) REVERT: B 142 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6767 (p90) REVERT: B 217 MET cc_start: 0.7464 (mtt) cc_final: 0.7254 (mtt) REVERT: B 219 ARG cc_start: 0.7660 (mmt90) cc_final: 0.7295 (mpt-90) REVERT: B 226 GLU cc_start: 0.7607 (pt0) cc_final: 0.7168 (pt0) REVERT: B 258 ASP cc_start: 0.7608 (t0) cc_final: 0.6800 (t0) REVERT: B 260 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: B 283 ARG cc_start: 0.8230 (tpt-90) cc_final: 0.7777 (tpt-90) REVERT: B 289 TYR cc_start: 0.8229 (m-80) cc_final: 0.7629 (m-80) REVERT: B 298 ASP cc_start: 0.7467 (t70) cc_final: 0.6683 (t0) REVERT: C 23 ASN cc_start: 0.8779 (t0) cc_final: 0.8551 (t0) REVERT: C 210 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7941 (p) REVERT: C 273 PHE cc_start: 0.8203 (t80) cc_final: 0.7953 (t80) REVERT: C 283 ARG cc_start: 0.7673 (mtt90) cc_final: 0.7335 (mtt90) REVERT: C 299 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: C 392 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6879 (mm-30) REVERT: G 13 ARG cc_start: 0.8006 (ptp-110) cc_final: 0.7322 (ptp-110) REVERT: N 38 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8409 (ptt180) REVERT: N 72 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7515 (ttm-80) outliers start: 58 outliers final: 42 residues processed: 313 average time/residue: 0.1324 time to fit residues: 51.8453 Evaluate side-chains 332 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109780 restraints weight = 13077.799| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.58 r_work: 0.3284 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8099 Z= 0.163 Angle : 0.617 7.800 11003 Z= 0.321 Chirality : 0.045 0.214 1265 Planarity : 0.003 0.047 1405 Dihedral : 4.250 18.451 1112 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 6.27 % Allowed : 34.67 % Favored : 59.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 0.65 (0.27), residues: 1008 helix: 1.99 (0.26), residues: 404 sheet: -0.04 (0.36), residues: 217 loop : -0.95 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.012 0.001 TYR N 95 PHE 0.008 0.001 PHE C 290 TRP 0.014 0.002 TRP B 211 HIS 0.006 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8096) covalent geometry : angle 0.61614 (10997) SS BOND : bond 0.00161 ( 3) SS BOND : angle 1.73476 ( 6) hydrogen bonds : bond 0.03573 ( 401) hydrogen bonds : angle 4.15954 ( 1164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 283 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7797 (mp) REVERT: A 118 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6605 (t0) REVERT: A 119 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7172 (tp) REVERT: A 157 SER cc_start: 0.8653 (m) cc_final: 0.8188 (p) REVERT: A 179 ARG cc_start: 0.7808 (tpp-160) cc_final: 0.7450 (tpp-160) REVERT: A 183 LEU cc_start: 0.8869 (tt) cc_final: 0.8267 (tp) REVERT: A 246 VAL cc_start: 0.8512 (t) cc_final: 0.8291 (p) REVERT: B 9 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7173 (pp30) REVERT: B 22 ARG cc_start: 0.8353 (mtm-85) cc_final: 0.7299 (mtm-85) REVERT: B 52 ARG cc_start: 0.7099 (mtm180) cc_final: 0.6809 (mtm180) REVERT: B 57 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8304 (ptpp) REVERT: B 100 VAL cc_start: 0.8472 (m) cc_final: 0.8232 (p) REVERT: B 118 ASP cc_start: 0.7640 (p0) cc_final: 0.7324 (p0) REVERT: B 226 GLU cc_start: 0.7582 (pt0) cc_final: 0.7164 (pt0) REVERT: B 258 ASP cc_start: 0.7584 (t0) cc_final: 0.6793 (t0) REVERT: B 260 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: B 283 ARG cc_start: 0.8216 (tpt-90) cc_final: 0.7746 (tpt-90) REVERT: B 289 TYR cc_start: 0.8218 (m-80) cc_final: 0.7550 (m-80) REVERT: B 298 ASP cc_start: 0.7465 (t70) cc_final: 0.6678 (t0) REVERT: C 23 ASN cc_start: 0.8779 (t0) cc_final: 0.8552 (t0) REVERT: C 273 PHE cc_start: 0.8216 (t80) cc_final: 0.7965 (t80) REVERT: C 283 ARG cc_start: 0.7652 (mtt90) cc_final: 0.7319 (mtt90) REVERT: C 299 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6233 (mp0) REVERT: C 392 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6874 (mm-30) REVERT: G 13 ARG cc_start: 0.7976 (ptp-110) cc_final: 0.7312 (ptp-110) REVERT: N 38 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8418 (ptt180) REVERT: N 72 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7511 (ttm-80) outliers start: 53 outliers final: 40 residues processed: 314 average time/residue: 0.1356 time to fit residues: 53.1008 Evaluate side-chains 332 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 283 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 0.0970 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.0470 chunk 69 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.127772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111386 restraints weight = 13016.783| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.59 r_work: 0.3307 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8099 Z= 0.125 Angle : 0.595 7.471 11003 Z= 0.309 Chirality : 0.044 0.211 1265 Planarity : 0.003 0.048 1405 Dihedral : 4.114 17.527 1112 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 6.27 % Allowed : 34.79 % Favored : 58.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 0.69 (0.27), residues: 1008 helix: 2.11 (0.26), residues: 401 sheet: 0.00 (0.36), residues: 211 loop : -1.02 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 232 TYR 0.009 0.001 TYR N 95 PHE 0.007 0.001 PHE B 222 TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8096) covalent geometry : angle 0.59456 (10997) SS BOND : bond 0.00129 ( 3) SS BOND : angle 0.79250 ( 6) hydrogen bonds : bond 0.03353 ( 401) hydrogen bonds : angle 4.07316 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2035.71 seconds wall clock time: 35 minutes 44.08 seconds (2144.08 seconds total)