Starting phenix.real_space_refine on Fri Aug 22 22:20:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wc9_37435/08_2025/8wc9_37435_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wc9_37435/08_2025/8wc9_37435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wc9_37435/08_2025/8wc9_37435_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wc9_37435/08_2025/8wc9_37435_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wc9_37435/08_2025/8wc9_37435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wc9_37435/08_2025/8wc9_37435.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 59 5.16 5 C 5350 2.51 5 N 1430 2.21 5 O 1554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 8394 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1801 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 5 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2521 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 4, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 56 Chain: "R" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1932 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 12, 'TRANS': 248} Chain breaks: 2 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2, 'ARG:plan': 4, 'GLU:plan': 4, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "S" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1737 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "Y" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 393 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'VMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.35, per 1000 atoms: 0.28 Number of scatterers: 8394 At special positions: 0 Unit cell: (87.55, 122.4, 121.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 59 16.00 O 1554 8.00 N 1430 7.00 C 5350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 0.90 Conformation dependent library (CDL) restraints added in 514.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 36.4% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.684A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.536A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.547A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 239' Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.177A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.502A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.666A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.566A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'R' and resid 25 through 28 Processing helix chain 'R' and resid 29 through 49 removed outlier: 3.585A pdb=" N ILE R 33 " --> pdb=" O MET R 29 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN R 40 " --> pdb=" O THR R 36 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N HIS R 49 " --> pdb=" O ILE R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 86 removed outlier: 3.531A pdb=" N TRP R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) Proline residue: R 77 - end of helix removed outlier: 4.087A pdb=" N GLU R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 125 removed outlier: 3.595A pdb=" N CYS R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 134 Processing helix chain 'R' and resid 135 through 156 removed outlier: 3.585A pdb=" N ILE R 139 " --> pdb=" O ASN R 135 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU R 140 " --> pdb=" O ILE R 136 " (cutoff:3.500A) Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 167 through 177 removed outlier: 3.974A pdb=" N TYR R 171 " --> pdb=" O VAL R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 198 removed outlier: 3.754A pdb=" N VAL R 191 " --> pdb=" O LYS R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 207 Processing helix chain 'R' and resid 207 through 220 removed outlier: 3.776A pdb=" N ARG R 211 " --> pdb=" O PHE R 207 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE R 212 " --> pdb=" O VAL R 208 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 275 removed outlier: 4.365A pdb=" N ILE R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET R 253 " --> pdb=" O THR R 249 " (cutoff:3.500A) Proline residue: R 263 - end of helix Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 279 through 303 removed outlier: 3.773A pdb=" N ASN R 283 " --> pdb=" O PRO R 279 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER R 294 " --> pdb=" O GLY R 290 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 310 Processing helix chain 'S' and resid 28 through 32 removed outlier: 4.023A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.756A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Y' and resid 35 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 213 removed outlier: 3.903A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 removed outlier: 6.300A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.861A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.800A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.724A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.598A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 191 removed outlier: 4.232A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.497A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.509A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.627A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.850A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR S 243 " --> pdb=" O TYR S 227 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.663A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1050 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: 1.33 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.33: 1698 1.33 - 1.48: 3286 1.48 - 1.63: 3505 1.63 - 1.79: 14 1.79 - 1.94: 72 Bond restraints: 8575 Sorted by residual: bond pdb=" CA ALA R 302 " pdb=" C ALA R 302 " ideal model delta sigma weight residual 1.525 1.449 0.076 1.11e-02 8.12e+03 4.67e+01 bond pdb=" C ASP R 126 " pdb=" O ASP R 126 " ideal model delta sigma weight residual 1.249 1.204 0.045 8.50e-03 1.38e+04 2.84e+01 bond pdb=" C ALA B 113 " pdb=" O ALA B 113 " ideal model delta sigma weight residual 1.234 1.176 0.058 1.26e-02 6.30e+03 2.11e+01 bond pdb=" C VAL R 208 " pdb=" O VAL R 208 " ideal model delta sigma weight residual 1.238 1.177 0.060 1.32e-02 5.74e+03 2.09e+01 bond pdb=" C GLY B 116 " pdb=" O GLY B 116 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.35e-02 5.49e+03 2.02e+01 ... (remaining 8570 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 11319 2.41 - 4.82: 279 4.82 - 7.23: 41 7.23 - 9.64: 12 9.64 - 12.05: 2 Bond angle restraints: 11653 Sorted by residual: angle pdb=" N SER B 334 " pdb=" CA SER B 334 " pdb=" C SER B 334 " ideal model delta sigma weight residual 112.58 124.09 -11.51 1.22e+00 6.72e-01 8.91e+01 angle pdb=" N SER R 46 " pdb=" CA SER R 46 " pdb=" C SER R 46 " ideal model delta sigma weight residual 112.89 104.68 8.21 1.24e+00 6.50e-01 4.38e+01 angle pdb=" N ILE R 200 " pdb=" CA ILE R 200 " pdb=" CB ILE R 200 " ideal model delta sigma weight residual 110.50 114.57 -4.07 6.30e-01 2.52e+00 4.18e+01 angle pdb=" C ILE R 32 " pdb=" CA ILE R 32 " pdb=" CB ILE R 32 " ideal model delta sigma weight residual 111.88 104.01 7.87 1.28e+00 6.10e-01 3.78e+01 angle pdb=" N ASN B 119 " pdb=" CA ASN B 119 " pdb=" C ASN B 119 " ideal model delta sigma weight residual 111.74 119.77 -8.03 1.35e+00 5.49e-01 3.54e+01 ... (remaining 11648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.16: 4389 14.16 - 28.31: 441 28.31 - 42.46: 157 42.46 - 56.62: 32 56.62 - 70.77: 13 Dihedral angle restraints: 5032 sinusoidal: 1823 harmonic: 3209 Sorted by residual: dihedral pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CA SER B 334 " pdb=" CB SER B 334 " ideal model delta harmonic sigma weight residual 122.80 136.44 -13.64 0 2.50e+00 1.60e-01 2.98e+01 dihedral pdb=" C SER B 334 " pdb=" N SER B 334 " pdb=" CA SER B 334 " pdb=" CB SER B 334 " ideal model delta harmonic sigma weight residual -122.60 -135.71 13.11 0 2.50e+00 1.60e-01 2.75e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.43 35.57 1 1.00e+01 1.00e-02 1.79e+01 ... (remaining 5029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1273 0.121 - 0.241: 47 0.241 - 0.362: 9 0.362 - 0.482: 2 0.482 - 0.603: 1 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.09e+00 chirality pdb=" CA PRO R 298 " pdb=" N PRO R 298 " pdb=" C PRO R 298 " pdb=" CB PRO R 298 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CA ASN R 40 " pdb=" N ASN R 40 " pdb=" C ASN R 40 " pdb=" CB ASN R 40 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 1329 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 200 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO R 201 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO R 201 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO R 201 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 301 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C TYR R 301 " 0.057 2.00e-02 2.50e+03 pdb=" O TYR R 301 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA R 302 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 193 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C ALA R 193 " -0.043 2.00e-02 2.50e+03 pdb=" O ALA R 193 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE R 194 " 0.015 2.00e-02 2.50e+03 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1012 2.74 - 3.28: 7891 3.28 - 3.82: 12822 3.82 - 4.36: 15008 4.36 - 4.90: 26922 Nonbonded interactions: 63655 Sorted by model distance: nonbonded pdb=" OG1 THR R 55 " pdb=" OD1 ASN R 58 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.217 3.040 nonbonded pdb=" ND2 ASN B 119 " pdb=" O THR B 143 " model vdw 2.281 3.120 nonbonded pdb=" NH1 ARG S 180 " pdb=" OE1 GLN S 186 " model vdw 2.286 3.120 nonbonded pdb=" NE2 GLN S 3 " pdb=" OG SER S 25 " model vdw 2.289 3.120 ... (remaining 63650 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: 1.060 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 9.700 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 8578 Z= 0.442 Angle : 0.907 12.047 11659 Z= 0.575 Chirality : 0.064 0.603 1332 Planarity : 0.006 0.104 1480 Dihedral : 13.812 70.775 2949 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.16 % Allowed : 2.43 % Favored : 96.41 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.26), residues: 1079 helix: 0.73 (0.28), residues: 369 sheet: -0.03 (0.33), residues: 257 loop : -1.73 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 98 TYR 0.023 0.002 TYR R 287 PHE 0.017 0.002 PHE R 198 TRP 0.013 0.002 TRP R 307 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00735 ( 8575) covalent geometry : angle 0.90661 (11653) SS BOND : bond 0.00371 ( 3) SS BOND : angle 1.65520 ( 6) hydrogen bonds : bond 0.20900 ( 365) hydrogen bonds : angle 7.37397 ( 1050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7817 (ptmt) cc_final: 0.7296 (pttp) REVERT: A 390 GLU cc_start: 0.7904 (tp30) cc_final: 0.7703 (tp30) REVERT: B 301 LYS cc_start: 0.8614 (mtmm) cc_final: 0.8262 (mtmm) REVERT: R 50 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.5807 (t80) outliers start: 10 outliers final: 4 residues processed: 154 average time/residue: 0.0963 time to fit residues: 20.5009 Evaluate side-chains 133 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 191 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 44 GLN B 75 GLN B 340 ASN R 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.174133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129922 restraints weight = 10232.437| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.90 r_work: 0.3291 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8578 Z= 0.125 Angle : 0.562 6.599 11659 Z= 0.300 Chirality : 0.043 0.176 1332 Planarity : 0.004 0.042 1480 Dihedral : 5.569 64.020 1199 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.27 % Allowed : 9.15 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.26), residues: 1079 helix: 1.40 (0.29), residues: 362 sheet: 0.15 (0.33), residues: 269 loop : -1.83 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 280 TYR 0.022 0.001 TYR R 287 PHE 0.014 0.001 PHE R 303 TRP 0.011 0.001 TRP B 297 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8575) covalent geometry : angle 0.56171 (11653) SS BOND : bond 0.00430 ( 3) SS BOND : angle 0.79236 ( 6) hydrogen bonds : bond 0.04836 ( 365) hydrogen bonds : angle 5.10594 ( 1050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7498 (ptmt) cc_final: 0.6881 (pttp) REVERT: A 280 ARG cc_start: 0.7183 (ttp-110) cc_final: 0.6786 (ttp-110) REVERT: B 301 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8058 (mtmm) REVERT: R 50 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.5567 (t80) REVERT: R 119 ASP cc_start: 0.8496 (t0) cc_final: 0.8262 (t0) outliers start: 11 outliers final: 6 residues processed: 137 average time/residue: 0.1022 time to fit residues: 19.1020 Evaluate side-chains 127 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 191 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 0.2980 chunk 99 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 75 GLN B 239 ASN ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.175354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.130848 restraints weight = 10164.947| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.76 r_work: 0.3297 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8578 Z= 0.109 Angle : 0.511 5.814 11659 Z= 0.272 Chirality : 0.042 0.192 1332 Planarity : 0.004 0.040 1480 Dihedral : 5.007 63.467 1195 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.93 % Allowed : 13.79 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.26), residues: 1079 helix: 1.55 (0.29), residues: 364 sheet: 0.13 (0.32), residues: 279 loop : -1.67 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.019 0.001 TYR R 287 PHE 0.010 0.001 PHE B 199 TRP 0.009 0.001 TRP B 297 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8575) covalent geometry : angle 0.51029 (11653) SS BOND : bond 0.00433 ( 3) SS BOND : angle 0.85534 ( 6) hydrogen bonds : bond 0.04279 ( 365) hydrogen bonds : angle 4.65886 ( 1050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7537 (ptmt) cc_final: 0.6937 (pttp) REVERT: A 280 ARG cc_start: 0.7237 (ttp-110) cc_final: 0.6701 (ttp-110) REVERT: B 301 LYS cc_start: 0.8398 (mtmm) cc_final: 0.7994 (mtmm) REVERT: R 50 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.5653 (t80) REVERT: R 119 ASP cc_start: 0.8447 (t0) cc_final: 0.8222 (t0) outliers start: 8 outliers final: 2 residues processed: 139 average time/residue: 0.0958 time to fit residues: 18.3835 Evaluate side-chains 128 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 105 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 0.0010 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 271 ASN B 88 ASN B 259 GLN ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.175431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123770 restraints weight = 10125.936| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.69 r_work: 0.3314 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.002 0.025 8578 Z= 0.101 Angle : 0.492 5.928 11659 Z= 0.262 Chirality : 0.042 0.210 1332 Planarity : 0.003 0.039 1480 Dihedral : 4.375 54.028 1192 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.93 % Allowed : 15.53 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.26), residues: 1079 helix: 1.67 (0.29), residues: 365 sheet: 0.06 (0.32), residues: 282 loop : -1.55 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.021 0.001 TYR R 287 PHE 0.011 0.001 PHE A 376 TRP 0.008 0.001 TRP B 297 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 8575) covalent geometry : angle 0.49176 (11653) SS BOND : bond 0.00419 ( 3) SS BOND : angle 0.80697 ( 6) hydrogen bonds : bond 0.03839 ( 365) hydrogen bonds : angle 4.45774 ( 1050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7524 (ptmt) cc_final: 0.6937 (pttp) REVERT: A 307 LYS cc_start: 0.5551 (mmtt) cc_final: 0.5220 (mmtm) REVERT: B 301 LYS cc_start: 0.8319 (mtmm) cc_final: 0.8028 (mtmm) REVERT: R 42 ILE cc_start: 0.8123 (pt) cc_final: 0.7768 (pt) REVERT: R 50 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.5593 (t80) REVERT: R 119 ASP cc_start: 0.8397 (t0) cc_final: 0.8159 (t0) outliers start: 8 outliers final: 4 residues processed: 137 average time/residue: 0.0990 time to fit residues: 18.5112 Evaluate side-chains 131 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 44 GLN R 297 ASN S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.169638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117084 restraints weight = 10067.811| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.65 r_work: 0.3210 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8578 Z= 0.210 Angle : 0.611 8.880 11659 Z= 0.326 Chirality : 0.045 0.190 1332 Planarity : 0.004 0.038 1480 Dihedral : 4.940 53.551 1192 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.32 % Allowed : 16.11 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.26), residues: 1079 helix: 1.42 (0.28), residues: 364 sheet: -0.01 (0.32), residues: 275 loop : -1.59 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 280 TYR 0.018 0.002 TYR S 190 PHE 0.014 0.002 PHE A 376 TRP 0.014 0.001 TRP B 63 HIS 0.007 0.002 HIS R 62 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 8575) covalent geometry : angle 0.61023 (11653) SS BOND : bond 0.00551 ( 3) SS BOND : angle 1.20249 ( 6) hydrogen bonds : bond 0.05637 ( 365) hydrogen bonds : angle 4.76447 ( 1050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7698 (ptmt) cc_final: 0.7096 (pttp) REVERT: A 280 ARG cc_start: 0.7390 (ttp-110) cc_final: 0.7108 (ttp-110) REVERT: A 336 ARG cc_start: 0.5532 (ttt-90) cc_final: 0.5320 (mtp180) REVERT: B 325 MET cc_start: 0.7131 (mtt) cc_final: 0.6877 (mtm) REVERT: R 50 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.5511 (t80) REVERT: R 119 ASP cc_start: 0.8513 (t0) cc_final: 0.8237 (t0) outliers start: 20 outliers final: 14 residues processed: 140 average time/residue: 0.1034 time to fit residues: 19.6778 Evaluate side-chains 139 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 4 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.173252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.119750 restraints weight = 10145.158| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.77 r_work: 0.3249 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8578 Z= 0.124 Angle : 0.532 6.285 11659 Z= 0.283 Chirality : 0.042 0.196 1332 Planarity : 0.004 0.038 1480 Dihedral : 4.640 53.862 1192 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.20 % Allowed : 16.69 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.26), residues: 1079 helix: 1.63 (0.29), residues: 360 sheet: 0.03 (0.32), residues: 275 loop : -1.58 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 280 TYR 0.019 0.001 TYR R 287 PHE 0.011 0.001 PHE B 199 TRP 0.010 0.001 TRP B 63 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8575) covalent geometry : angle 0.53147 (11653) SS BOND : bond 0.00457 ( 3) SS BOND : angle 0.86811 ( 6) hydrogen bonds : bond 0.04508 ( 365) hydrogen bonds : angle 4.59540 ( 1050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7680 (ptmt) cc_final: 0.7075 (pttp) REVERT: A 307 LYS cc_start: 0.5855 (mmtt) cc_final: 0.5619 (mmtt) REVERT: B 273 ILE cc_start: 0.8848 (mt) cc_final: 0.8643 (mt) REVERT: B 325 MET cc_start: 0.7175 (mtt) cc_final: 0.6926 (mtm) REVERT: R 50 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.5468 (t80) REVERT: R 119 ASP cc_start: 0.8505 (t70) cc_final: 0.8241 (t0) outliers start: 19 outliers final: 14 residues processed: 141 average time/residue: 0.1139 time to fit residues: 21.4416 Evaluate side-chains 138 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN R 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.171925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118087 restraints weight = 10353.010| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.80 r_work: 0.3223 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8578 Z= 0.158 Angle : 0.556 6.741 11659 Z= 0.297 Chirality : 0.043 0.199 1332 Planarity : 0.004 0.037 1480 Dihedral : 4.700 50.953 1192 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.32 % Allowed : 17.61 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.26), residues: 1079 helix: 1.56 (0.29), residues: 361 sheet: 0.10 (0.33), residues: 269 loop : -1.59 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 280 TYR 0.017 0.002 TYR R 287 PHE 0.012 0.001 PHE B 199 TRP 0.012 0.001 TRP B 63 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8575) covalent geometry : angle 0.55578 (11653) SS BOND : bond 0.00491 ( 3) SS BOND : angle 0.97189 ( 6) hydrogen bonds : bond 0.04889 ( 365) hydrogen bonds : angle 4.61892 ( 1050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7793 (ptmt) cc_final: 0.7095 (pttp) REVERT: A 339 TYR cc_start: 0.7211 (m-80) cc_final: 0.6744 (m-80) REVERT: B 273 ILE cc_start: 0.8870 (mt) cc_final: 0.8670 (mt) REVERT: B 325 MET cc_start: 0.7211 (mtt) cc_final: 0.6994 (mtm) REVERT: R 50 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.5322 (t80) REVERT: R 119 ASP cc_start: 0.8530 (t70) cc_final: 0.8261 (t0) outliers start: 20 outliers final: 16 residues processed: 139 average time/residue: 0.1022 time to fit residues: 19.2931 Evaluate side-chains 139 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 75 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 33 optimal weight: 0.0060 chunk 6 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.173887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.121572 restraints weight = 9933.076| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.68 r_work: 0.3273 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8578 Z= 0.113 Angle : 0.524 7.395 11659 Z= 0.280 Chirality : 0.042 0.203 1332 Planarity : 0.004 0.038 1480 Dihedral : 4.468 51.068 1192 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.62 % Allowed : 18.08 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.26), residues: 1079 helix: 1.72 (0.29), residues: 361 sheet: 0.10 (0.32), residues: 275 loop : -1.48 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 280 TYR 0.011 0.001 TYR S 190 PHE 0.010 0.001 PHE B 199 TRP 0.008 0.001 TRP A 234 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8575) covalent geometry : angle 0.52401 (11653) SS BOND : bond 0.00408 ( 3) SS BOND : angle 0.75967 ( 6) hydrogen bonds : bond 0.04073 ( 365) hydrogen bonds : angle 4.46348 ( 1050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7667 (ptmt) cc_final: 0.7110 (pttp) REVERT: A 339 TYR cc_start: 0.7075 (m-80) cc_final: 0.6633 (m-80) REVERT: A 378 ASP cc_start: 0.7453 (m-30) cc_final: 0.6937 (m-30) REVERT: B 325 MET cc_start: 0.7092 (mtt) cc_final: 0.6713 (mmt) REVERT: R 50 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.5373 (t80) REVERT: R 119 ASP cc_start: 0.8514 (t70) cc_final: 0.8245 (t0) outliers start: 14 outliers final: 13 residues processed: 141 average time/residue: 0.1048 time to fit residues: 20.0981 Evaluate side-chains 139 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.174674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122927 restraints weight = 9976.779| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.66 r_work: 0.3301 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8578 Z= 0.100 Angle : 0.503 6.409 11659 Z= 0.268 Chirality : 0.042 0.208 1332 Planarity : 0.003 0.038 1480 Dihedral : 4.237 50.395 1192 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.27 % Allowed : 18.31 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.26), residues: 1079 helix: 1.90 (0.29), residues: 361 sheet: 0.09 (0.32), residues: 273 loop : -1.44 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 280 TYR 0.020 0.001 TYR R 287 PHE 0.009 0.001 PHE B 199 TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 8575) covalent geometry : angle 0.50262 (11653) SS BOND : bond 0.00397 ( 3) SS BOND : angle 0.71208 ( 6) hydrogen bonds : bond 0.03655 ( 365) hydrogen bonds : angle 4.31889 ( 1050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7619 (ptmt) cc_final: 0.7068 (pttp) REVERT: A 339 TYR cc_start: 0.6973 (m-80) cc_final: 0.6603 (m-80) REVERT: A 378 ASP cc_start: 0.7449 (m-30) cc_final: 0.6943 (m-30) REVERT: B 325 MET cc_start: 0.7028 (mtt) cc_final: 0.6627 (mtm) REVERT: R 50 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.5231 (t80) REVERT: R 119 ASP cc_start: 0.8392 (t70) cc_final: 0.8150 (t0) outliers start: 11 outliers final: 8 residues processed: 145 average time/residue: 0.0994 time to fit residues: 19.5392 Evaluate side-chains 139 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 0.0170 chunk 16 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 69 optimal weight: 0.1980 chunk 70 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.175604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.132484 restraints weight = 10038.794| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.87 r_work: 0.3293 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8578 Z= 0.102 Angle : 0.511 7.963 11659 Z= 0.271 Chirality : 0.042 0.202 1332 Planarity : 0.003 0.037 1480 Dihedral : 4.176 50.294 1192 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.51 % Allowed : 18.42 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.26), residues: 1079 helix: 1.97 (0.29), residues: 357 sheet: 0.11 (0.32), residues: 273 loop : -1.45 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 280 TYR 0.022 0.001 TYR R 287 PHE 0.008 0.001 PHE A 376 TRP 0.008 0.001 TRP A 234 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8575) covalent geometry : angle 0.51089 (11653) SS BOND : bond 0.00397 ( 3) SS BOND : angle 0.69465 ( 6) hydrogen bonds : bond 0.03680 ( 365) hydrogen bonds : angle 4.27556 ( 1050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7686 (ptmt) cc_final: 0.7144 (pttp) REVERT: A 339 TYR cc_start: 0.6975 (m-80) cc_final: 0.6634 (m-80) REVERT: A 378 ASP cc_start: 0.7439 (m-30) cc_final: 0.6960 (m-30) REVERT: B 325 MET cc_start: 0.7044 (mtt) cc_final: 0.6668 (mtm) REVERT: R 50 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.5155 (t80) REVERT: R 119 ASP cc_start: 0.8433 (t70) cc_final: 0.8218 (t0) REVERT: S 18 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7439 (mmm160) outliers start: 13 outliers final: 11 residues processed: 142 average time/residue: 0.1028 time to fit residues: 19.7955 Evaluate side-chains 146 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 8 optimal weight: 0.0000 chunk 46 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.174729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130285 restraints weight = 9901.198| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.71 r_work: 0.3304 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 8578 Z= 0.149 Angle : 0.882 59.171 11659 Z= 0.522 Chirality : 0.043 0.298 1332 Planarity : 0.004 0.037 1480 Dihedral : 4.174 50.264 1192 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.85 % Allowed : 17.84 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.26), residues: 1079 helix: 1.96 (0.29), residues: 357 sheet: 0.12 (0.32), residues: 273 loop : -1.46 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 280 TYR 0.021 0.001 TYR R 287 PHE 0.009 0.001 PHE A 376 TRP 0.008 0.001 TRP A 234 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8575) covalent geometry : angle 0.88207 (11653) SS BOND : bond 0.00382 ( 3) SS BOND : angle 0.72041 ( 6) hydrogen bonds : bond 0.03723 ( 365) hydrogen bonds : angle 4.27696 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2317.06 seconds wall clock time: 40 minutes 21.35 seconds (2421.35 seconds total)