Starting phenix.real_space_refine on Sat Aug 23 02:38:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jir_36325/08_2025/8jir_36325.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jir_36325/08_2025/8jir_36325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jir_36325/08_2025/8jir_36325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jir_36325/08_2025/8jir_36325.map" model { file = "/net/cci-nas-00/data/ceres_data/8jir_36325/08_2025/8jir_36325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jir_36325/08_2025/8jir_36325.cif" } resolution = 2.57 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= 0.020 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 56 5.16 5 C 5731 2.51 5 N 1556 2.21 5 O 1671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9014 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1884 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2581 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2886 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 13, 'TRANS': 369} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 401 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 6, 'ARG:plan': 6, 'ASP:plan': 5, 'PHE:plan': 4, 'ASN:plan1': 3, 'TYR:plan': 3, 'TRP:plan': 4, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 206 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.04, per 1000 atoms: 0.23 Number of scatterers: 9014 At special positions: 0 Unit cell: (80.325, 100.674, 175.644, 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 56 16.00 O 1671 8.00 N 1556 7.00 C 5731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.04 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.02 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 277.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 39.2% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 removed outlier: 4.288A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.549A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 removed outlier: 3.658A pdb=" N ASP A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 300 through 319 removed outlier: 3.682A pdb=" N TYR A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 removed outlier: 3.614A pdb=" N VAL A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 24 Processing helix chain 'B' and resid 2 through 23 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.655A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'R' and resid 31 through 53 Processing helix chain 'R' and resid 89 through 94 removed outlier: 4.731A pdb=" N SER R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 169 removed outlier: 3.531A pdb=" N ALA R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 200 Processing helix chain 'R' and resid 207 through 215 Processing helix chain 'R' and resid 223 through 257 removed outlier: 3.665A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU R 247 " --> pdb=" O TRP R 243 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU R 255 " --> pdb=" O LEU R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 276 removed outlier: 3.931A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 292 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 303 through 309 removed outlier: 3.758A pdb=" N ILE R 308 " --> pdb=" O TYR R 305 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE R 309 " --> pdb=" O TRP R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 338 Processing helix chain 'R' and resid 344 through 361 removed outlier: 3.733A pdb=" N ARG R 348 " --> pdb=" O ASP R 344 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 366 removed outlier: 3.765A pdb=" N ILE R 366 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 404 removed outlier: 4.239A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 419 removed outlier: 3.569A pdb=" N PHE R 413 " --> pdb=" O VAL R 409 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.197A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.513A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.641A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.714A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.712A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 158 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.189A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.049A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.425A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.937A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 80 through 82 432 hydrogen bonds defined for protein. 1239 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: 1.17 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1526 1.32 - 1.45: 2718 1.45 - 1.58: 4881 1.58 - 1.72: 0 1.72 - 1.85: 76 Bond restraints: 9201 Sorted by residual: bond pdb=" CA ARG B 150 " pdb=" C ARG B 150 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.04e-02 9.25e+03 3.20e+01 bond pdb=" CA GLY B 244 " pdb=" C GLY B 244 " ideal model delta sigma weight residual 1.520 1.480 0.041 7.30e-03 1.88e+04 3.09e+01 bond pdb=" CA TYR N 32 " pdb=" C TYR N 32 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.21e-02 6.83e+03 2.40e+01 bond pdb=" C ARG B 150 " pdb=" O ARG B 150 " ideal model delta sigma weight residual 1.234 1.183 0.051 1.07e-02 8.73e+03 2.30e+01 bond pdb=" CA ILE B 58 " pdb=" C ILE B 58 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.19e-02 7.06e+03 1.33e+01 ... (remaining 9196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 12097 2.58 - 5.16: 316 5.16 - 7.74: 54 7.74 - 10.33: 9 10.33 - 12.91: 3 Bond angle restraints: 12479 Sorted by residual: angle pdb=" N GLY A 183 " pdb=" CA GLY A 183 " pdb=" C GLY A 183 " ideal model delta sigma weight residual 111.67 120.86 -9.19 9.20e-01 1.18e+00 9.97e+01 angle pdb=" N ASP R 122 " pdb=" CA ASP R 122 " pdb=" C ASP R 122 " ideal model delta sigma weight residual 113.19 101.88 11.31 1.19e+00 7.06e-01 9.04e+01 angle pdb=" N GLU R 125 " pdb=" CA GLU R 125 " pdb=" C GLU R 125 " ideal model delta sigma weight residual 109.62 96.71 12.91 1.50e+00 4.44e-01 7.40e+01 angle pdb=" N LEU R 32 " pdb=" CA LEU R 32 " pdb=" C LEU R 32 " ideal model delta sigma weight residual 111.14 103.47 7.67 1.08e+00 8.57e-01 5.04e+01 angle pdb=" N LEU B 152 " pdb=" CA LEU B 152 " pdb=" C LEU B 152 " ideal model delta sigma weight residual 111.14 104.00 7.14 1.08e+00 8.57e-01 4.38e+01 ... (remaining 12474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4875 17.97 - 35.94: 410 35.94 - 53.90: 127 53.90 - 71.87: 26 71.87 - 89.84: 17 Dihedral angle restraints: 5455 sinusoidal: 2055 harmonic: 3400 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual 93.00 -177.16 -89.84 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 154.60 -61.60 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 151.41 -58.41 1 1.00e+01 1.00e-02 4.57e+01 ... (remaining 5452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1272 0.099 - 0.197: 111 0.197 - 0.296: 19 0.296 - 0.395: 2 0.395 - 0.494: 2 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CA ASN B 155 " pdb=" N ASN B 155 " pdb=" C ASN B 155 " pdb=" CB ASN B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.09e+00 chirality pdb=" CA HIS B 142 " pdb=" N HIS B 142 " pdb=" C HIS B 142 " pdb=" CB HIS B 142 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CA ILE B 37 " pdb=" N ILE B 37 " pdb=" C ILE B 37 " pdb=" CB ILE B 37 " both_signs ideal model delta sigma weight residual False 2.43 2.05 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 1403 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 D6M P 101 " -0.045 2.00e-02 2.50e+03 7.63e-02 7.28e+01 pdb=" C04 D6M P 101 " 0.092 2.00e-02 2.50e+03 pdb=" C12 D6M P 101 " 0.075 2.00e-02 2.50e+03 pdb=" N03 D6M P 101 " -0.114 2.00e-02 2.50e+03 pdb=" O01 D6M P 101 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 205 " -0.023 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C TYR R 205 " 0.081 2.00e-02 2.50e+03 pdb=" O TYR R 205 " -0.031 2.00e-02 2.50e+03 pdb=" N SER R 206 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 57 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C LYS B 57 " -0.064 2.00e-02 2.50e+03 pdb=" O LYS B 57 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE B 58 " 0.021 2.00e-02 2.50e+03 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 72 2.56 - 3.14: 7542 3.14 - 3.73: 14011 3.73 - 4.31: 19759 4.31 - 4.90: 32539 Nonbonded interactions: 73923 Sorted by model distance: nonbonded pdb=" OE1 GLU P 15 " pdb=" OH TYR R 205 " model vdw 1.972 3.040 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR N 28 " pdb=" CE1 TYR N 32 " model vdw 2.221 3.340 nonbonded pdb=" NH2 ARG A 205 " pdb=" OD1 ASP B 186 " model vdw 2.221 3.120 ... (remaining 73918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.730 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.010 0.097 9207 Z= 0.579 Angle : 1.024 12.907 12489 Z= 0.643 Chirality : 0.065 0.494 1406 Planarity : 0.006 0.083 1590 Dihedral : 15.934 87.516 3240 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.95 % Favored : 92.53 % Rotamer: Outliers : 6.61 % Allowed : 3.47 % Favored : 89.92 % Cbeta Deviations : 0.27 % 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: -1.76 (0.24), residues: 1151 helix: 0.14 (0.25), residues: 434 sheet: -1.47 (0.32), residues: 236 loop : -2.20 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 98 TYR 0.033 0.003 TYR N 117 PHE 0.024 0.002 PHE B 151 TRP 0.012 0.002 TRP A 248 HIS 0.012 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00989 ( 9201) covalent geometry : angle 1.02338 (12479) SS BOND : bond 0.00575 ( 5) SS BOND : angle 1.39525 ( 10) hydrogen bonds : bond 0.20227 ( 432) hydrogen bonds : angle 8.06842 ( 1239) Misc. bond : bond 0.09722 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 0.370 Fit side-chains REVERT: A 226 ASP cc_start: 0.8592 (t0) cc_final: 0.8311 (t0) REVERT: A 266 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8526 (mp0) REVERT: A 274 LYS cc_start: 0.8918 (pptt) cc_final: 0.8677 (pptt) REVERT: P 27 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.9005 (mmtt) REVERT: B 260 GLU cc_start: 0.8215 (pt0) cc_final: 0.7744 (pm20) REVERT: B 280 LYS cc_start: 0.8841 (tmtt) cc_final: 0.8537 (tmtt) REVERT: B 338 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8537 (mm) REVERT: G 36 ASP cc_start: 0.8284 (m-30) cc_final: 0.7992 (m-30) REVERT: N 117 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: N 123 GLN cc_start: 0.8262 (tp-100) cc_final: 0.8030 (tm-30) REVERT: N 124 VAL cc_start: 0.7635 (OUTLIER) cc_final: 0.7097 (p) REVERT: N 125 THR cc_start: 0.8974 (m) cc_final: 0.8413 (m) REVERT: R 222 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8321 (p0) outliers start: 61 outliers final: 13 residues processed: 205 average time/residue: 0.5650 time to fit residues: 122.7869 Evaluate side-chains 146 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 14 LYS Chi-restraints excluded: chain P residue 27 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 197 LYS Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN R 140 GLN R 171 HIS R 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.114157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.078606 restraints weight = 15949.707| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.20 r_work: 0.2932 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.004 0.033 9207 Z= 0.169 Angle : 0.640 8.638 12489 Z= 0.342 Chirality : 0.044 0.242 1406 Planarity : 0.005 0.060 1590 Dihedral : 8.948 89.137 1322 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.00 % Favored : 95.74 % Rotamer: Outliers : 2.93 % Allowed : 14.84 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.25), residues: 1151 helix: 1.28 (0.25), residues: 440 sheet: -1.50 (0.31), residues: 242 loop : -1.71 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 197 TYR 0.025 0.002 TYR N 60 PHE 0.014 0.001 PHE B 151 TRP 0.016 0.001 TRP R 214 HIS 0.006 0.001 HIS R 173 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9201) covalent geometry : angle 0.63836 (12479) SS BOND : bond 0.00452 ( 5) SS BOND : angle 1.53401 ( 10) hydrogen bonds : bond 0.04696 ( 432) hydrogen bonds : angle 5.29487 ( 1239) Misc. bond : bond 0.00067 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.366 Fit side-chains REVERT: A 207 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8468 (mt-10) REVERT: A 226 ASP cc_start: 0.8655 (t0) cc_final: 0.8439 (t0) REVERT: A 235 GLU cc_start: 0.8662 (tp30) cc_final: 0.8091 (tp30) REVERT: A 266 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8665 (mp0) REVERT: A 274 LYS cc_start: 0.9056 (pptt) cc_final: 0.8768 (pptt) REVERT: P 27 LYS cc_start: 0.9302 (mtmm) cc_final: 0.8873 (mmtt) REVERT: B 59 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: B 215 GLU cc_start: 0.8499 (pm20) cc_final: 0.8024 (pm20) REVERT: B 260 GLU cc_start: 0.8365 (pt0) cc_final: 0.7877 (pm20) REVERT: B 268 ASN cc_start: 0.8836 (m110) cc_final: 0.8608 (m110) REVERT: N 46 GLU cc_start: 0.8176 (tp30) cc_final: 0.7913 (pt0) REVERT: N 50 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7608 (p0) REVERT: N 80 TYR cc_start: 0.7961 (m-80) cc_final: 0.7690 (m-80) REVERT: N 117 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: N 123 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7893 (tm-30) REVERT: N 124 VAL cc_start: 0.7028 (OUTLIER) cc_final: 0.6741 (p) REVERT: R 33 TRP cc_start: 0.8811 (t-100) cc_final: 0.8568 (t-100) REVERT: R 265 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7871 (tp) REVERT: R 408 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8121 (mt-10) outliers start: 27 outliers final: 9 residues processed: 166 average time/residue: 0.6222 time to fit residues: 109.4612 Evaluate side-chains 153 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain R residue 409 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 40.0000 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 chunk 39 optimal weight: 0.0870 chunk 63 optimal weight: 7.9990 chunk 60 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 32 GLN G 11 GLN N 77 ASN R 140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.115878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.080458 restraints weight = 15944.677| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.24 r_work: 0.2988 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9207 Z= 0.122 Angle : 0.558 6.922 12489 Z= 0.296 Chirality : 0.042 0.157 1406 Planarity : 0.004 0.052 1590 Dihedral : 7.752 89.515 1294 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.82 % Favored : 96.09 % Rotamer: Outliers : 2.60 % Allowed : 18.09 % Favored : 79.31 % 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: -0.48 (0.25), residues: 1151 helix: 1.59 (0.25), residues: 444 sheet: -1.30 (0.32), residues: 232 loop : -1.66 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 284 TYR 0.020 0.002 TYR N 60 PHE 0.012 0.001 PHE B 151 TRP 0.027 0.001 TRP R 120 HIS 0.004 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9201) covalent geometry : angle 0.55710 (12479) SS BOND : bond 0.00292 ( 5) SS BOND : angle 1.02128 ( 10) hydrogen bonds : bond 0.03835 ( 432) hydrogen bonds : angle 4.72879 ( 1239) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8596 (t0) cc_final: 0.8222 (t0) REVERT: A 226 ASP cc_start: 0.8577 (t0) cc_final: 0.8359 (t0) REVERT: A 235 GLU cc_start: 0.8496 (tp30) cc_final: 0.7842 (tp30) REVERT: A 272 LYS cc_start: 0.9173 (mppt) cc_final: 0.8941 (mppt) REVERT: A 274 LYS cc_start: 0.9144 (pptt) cc_final: 0.8883 (pptt) REVERT: B 61 MET cc_start: 0.9101 (pp-130) cc_final: 0.8768 (pp-130) REVERT: B 228 ASP cc_start: 0.8318 (m-30) cc_final: 0.7793 (m-30) REVERT: B 260 GLU cc_start: 0.8293 (pt0) cc_final: 0.7797 (pm20) REVERT: B 268 ASN cc_start: 0.8833 (m110) cc_final: 0.8627 (m110) REVERT: B 280 LYS cc_start: 0.8781 (tmtt) cc_final: 0.8446 (tmtt) REVERT: B 301 LYS cc_start: 0.7780 (mptt) cc_final: 0.7565 (mmtm) REVERT: G 46 LYS cc_start: 0.8887 (ttpm) cc_final: 0.8674 (tppt) REVERT: N 46 GLU cc_start: 0.8108 (tp30) cc_final: 0.7854 (pt0) REVERT: N 80 TYR cc_start: 0.7961 (m-80) cc_final: 0.7580 (m-80) REVERT: N 106 ASP cc_start: 0.8576 (p0) cc_final: 0.8280 (p0) REVERT: N 123 GLN cc_start: 0.8050 (tp-100) cc_final: 0.7820 (tm-30) REVERT: R 265 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7835 (tp) REVERT: R 308 ILE cc_start: 0.8801 (pt) cc_final: 0.8585 (pp) REVERT: R 338 ASN cc_start: 0.7157 (t0) cc_final: 0.6555 (t0) REVERT: R 408 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8105 (mt-10) REVERT: R 409 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8352 (p) outliers start: 24 outliers final: 10 residues processed: 171 average time/residue: 0.5929 time to fit residues: 108.0860 Evaluate side-chains 154 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain R residue 409 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 79 optimal weight: 40.0000 chunk 102 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 340 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.114719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.079218 restraints weight = 16181.978| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.23 r_work: 0.2955 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9207 Z= 0.150 Angle : 0.570 7.789 12489 Z= 0.303 Chirality : 0.043 0.206 1406 Planarity : 0.004 0.046 1590 Dihedral : 7.419 89.006 1289 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.82 % Favored : 96.09 % Rotamer: Outliers : 2.60 % Allowed : 20.59 % Favored : 76.81 % 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: -0.25 (0.25), residues: 1151 helix: 1.85 (0.25), residues: 444 sheet: -1.25 (0.32), residues: 234 loop : -1.56 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 96 TYR 0.022 0.002 TYR R 42 PHE 0.011 0.001 PHE R 324 TRP 0.012 0.001 TRP R 120 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9201) covalent geometry : angle 0.56921 (12479) SS BOND : bond 0.00230 ( 5) SS BOND : angle 0.92723 ( 10) hydrogen bonds : bond 0.03807 ( 432) hydrogen bonds : angle 4.59086 ( 1239) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.453 Fit side-chains REVERT: A 190 GLN cc_start: 0.9252 (tt0) cc_final: 0.8887 (tt0) REVERT: A 206 ASP cc_start: 0.8644 (t0) cc_final: 0.8279 (t0) REVERT: A 226 ASP cc_start: 0.8578 (t0) cc_final: 0.8342 (t0) REVERT: A 235 GLU cc_start: 0.8467 (tp30) cc_final: 0.7926 (tp30) REVERT: A 274 LYS cc_start: 0.9203 (pptt) cc_final: 0.8992 (pptt) REVERT: P 27 LYS cc_start: 0.9342 (mtmm) cc_final: 0.8831 (mmtt) REVERT: B 215 GLU cc_start: 0.8359 (pm20) cc_final: 0.8024 (pm20) REVERT: B 217 MET cc_start: 0.8174 (pmt) cc_final: 0.7902 (pmt) REVERT: B 228 ASP cc_start: 0.8351 (m-30) cc_final: 0.7919 (m-30) REVERT: B 260 GLU cc_start: 0.8351 (pt0) cc_final: 0.7846 (pm20) REVERT: B 268 ASN cc_start: 0.8808 (m110) cc_final: 0.8592 (m110) REVERT: B 280 LYS cc_start: 0.8799 (tmtt) cc_final: 0.8579 (tmtt) REVERT: B 301 LYS cc_start: 0.8012 (mptt) cc_final: 0.7803 (mmtm) REVERT: G 46 LYS cc_start: 0.8962 (ttpm) cc_final: 0.8714 (tppt) REVERT: G 50 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7773 (mm) REVERT: N 80 TYR cc_start: 0.7993 (m-80) cc_final: 0.7666 (m-80) REVERT: N 123 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7842 (tm-30) REVERT: R 265 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7852 (tp) REVERT: R 308 ILE cc_start: 0.8888 (pt) cc_final: 0.8662 (pp) REVERT: R 408 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8112 (mt-10) outliers start: 24 outliers final: 10 residues processed: 156 average time/residue: 0.6331 time to fit residues: 105.0694 Evaluate side-chains 152 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 265 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 93 optimal weight: 0.0970 chunk 7 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN R 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.114805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.079462 restraints weight = 16079.467| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.24 r_work: 0.2960 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9207 Z= 0.143 Angle : 0.551 5.991 12489 Z= 0.295 Chirality : 0.041 0.137 1406 Planarity : 0.004 0.043 1590 Dihedral : 7.222 87.617 1287 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.82 % Allowed : 21.13 % Favored : 76.06 % 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: 0.05 (0.25), residues: 1151 helix: 2.21 (0.25), residues: 433 sheet: -1.16 (0.31), residues: 239 loop : -1.39 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.019 0.002 TYR R 148 PHE 0.011 0.001 PHE R 324 TRP 0.014 0.001 TRP R 214 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9201) covalent geometry : angle 0.55077 (12479) SS BOND : bond 0.00212 ( 5) SS BOND : angle 0.86852 ( 10) hydrogen bonds : bond 0.03662 ( 432) hydrogen bonds : angle 4.46719 ( 1239) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.346 Fit side-chains REVERT: A 20 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8338 (mm-30) REVERT: A 200 ASP cc_start: 0.7992 (t0) cc_final: 0.7724 (OUTLIER) REVERT: A 206 ASP cc_start: 0.8700 (t0) cc_final: 0.8324 (t0) REVERT: A 226 ASP cc_start: 0.8631 (t0) cc_final: 0.8402 (t0) REVERT: A 235 GLU cc_start: 0.8458 (tp30) cc_final: 0.7723 (tp30) REVERT: A 274 LYS cc_start: 0.9239 (pptt) cc_final: 0.9021 (pptt) REVERT: P 27 LYS cc_start: 0.9367 (mtmm) cc_final: 0.8876 (mmtt) REVERT: B 17 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7736 (tm-30) REVERT: B 45 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8322 (mtp) REVERT: B 217 MET cc_start: 0.8111 (pmt) cc_final: 0.7886 (pmm) REVERT: B 228 ASP cc_start: 0.8331 (m-30) cc_final: 0.7821 (m-30) REVERT: B 260 GLU cc_start: 0.8364 (pt0) cc_final: 0.7819 (pm20) REVERT: B 268 ASN cc_start: 0.8779 (m110) cc_final: 0.8561 (m110) REVERT: B 280 LYS cc_start: 0.8820 (tmtt) cc_final: 0.8609 (tmtt) REVERT: B 301 LYS cc_start: 0.8051 (mptt) cc_final: 0.7820 (mmtm) REVERT: G 42 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8119 (mp0) REVERT: G 46 LYS cc_start: 0.8962 (ttpm) cc_final: 0.8714 (tppt) REVERT: G 50 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7709 (mm) REVERT: N 46 GLU cc_start: 0.8114 (tp30) cc_final: 0.7868 (pt0) REVERT: N 80 TYR cc_start: 0.7940 (m-80) cc_final: 0.7635 (m-80) REVERT: N 87 LYS cc_start: 0.7649 (ttmm) cc_final: 0.7306 (ttmt) REVERT: R 265 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7825 (tp) REVERT: R 308 ILE cc_start: 0.8901 (pt) cc_final: 0.8685 (pp) REVERT: R 408 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8084 (mt-10) outliers start: 26 outliers final: 13 residues processed: 156 average time/residue: 0.6076 time to fit residues: 100.7959 Evaluate side-chains 152 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 70 optimal weight: 0.3980 chunk 100 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 82 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN N 77 ASN R 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.115830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.080409 restraints weight = 16116.734| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.24 r_work: 0.2976 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9207 Z= 0.118 Angle : 0.545 6.702 12489 Z= 0.291 Chirality : 0.041 0.145 1406 Planarity : 0.004 0.040 1590 Dihedral : 7.071 85.867 1287 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.82 % Allowed : 21.78 % Favored : 75.41 % 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: 0.20 (0.25), residues: 1151 helix: 2.36 (0.26), residues: 433 sheet: -1.09 (0.31), residues: 239 loop : -1.32 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.018 0.001 TYR R 148 PHE 0.010 0.001 PHE R 324 TRP 0.012 0.001 TRP R 214 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9201) covalent geometry : angle 0.54493 (12479) SS BOND : bond 0.00198 ( 5) SS BOND : angle 0.74459 ( 10) hydrogen bonds : bond 0.03477 ( 432) hydrogen bonds : angle 4.38471 ( 1239) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.387 Fit side-chains REVERT: A 20 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8290 (mm-30) REVERT: A 200 ASP cc_start: 0.7967 (t0) cc_final: 0.7702 (OUTLIER) REVERT: A 206 ASP cc_start: 0.8697 (t0) cc_final: 0.8335 (t0) REVERT: A 235 GLU cc_start: 0.8426 (tp30) cc_final: 0.7834 (tp30) REVERT: A 274 LYS cc_start: 0.9241 (pptt) cc_final: 0.9031 (pptt) REVERT: P 27 LYS cc_start: 0.9359 (mtmm) cc_final: 0.8859 (mmtt) REVERT: B 45 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8314 (mtp) REVERT: B 215 GLU cc_start: 0.8367 (pm20) cc_final: 0.8044 (pm20) REVERT: B 217 MET cc_start: 0.8079 (pmt) cc_final: 0.7801 (pmt) REVERT: B 228 ASP cc_start: 0.8261 (m-30) cc_final: 0.7722 (m-30) REVERT: B 260 GLU cc_start: 0.8335 (pt0) cc_final: 0.7771 (pm20) REVERT: B 268 ASN cc_start: 0.8772 (m110) cc_final: 0.8546 (m110) REVERT: G 46 LYS cc_start: 0.8948 (ttpm) cc_final: 0.8731 (tppt) REVERT: G 50 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7756 (mm) REVERT: N 38 ARG cc_start: 0.8825 (ptt180) cc_final: 0.8497 (ptm-80) REVERT: N 80 TYR cc_start: 0.7918 (m-80) cc_final: 0.7562 (m-80) REVERT: R 204 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.5992 (pmt) REVERT: R 221 GLN cc_start: 0.8426 (mt0) cc_final: 0.8038 (mm-40) REVERT: R 265 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7814 (tp) REVERT: R 408 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8089 (mt-10) outliers start: 26 outliers final: 14 residues processed: 159 average time/residue: 0.6150 time to fit residues: 104.2152 Evaluate side-chains 157 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 0.0060 chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 79 optimal weight: 0.0050 chunk 67 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.116136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.081019 restraints weight = 16056.017| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.21 r_work: 0.2988 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9207 Z= 0.114 Angle : 0.550 10.756 12489 Z= 0.292 Chirality : 0.041 0.128 1406 Planarity : 0.004 0.040 1590 Dihedral : 6.822 82.833 1287 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.60 % Allowed : 22.86 % Favored : 74.54 % 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: 1151 helix: 2.43 (0.26), residues: 433 sheet: -0.95 (0.31), residues: 237 loop : -1.29 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.017 0.001 TYR R 148 PHE 0.010 0.001 PHE R 324 TRP 0.014 0.001 TRP R 214 HIS 0.003 0.000 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9201) covalent geometry : angle 0.54974 (12479) SS BOND : bond 0.00181 ( 5) SS BOND : angle 0.71923 ( 10) hydrogen bonds : bond 0.03369 ( 432) hydrogen bonds : angle 4.30792 ( 1239) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.425 Fit side-chains REVERT: A 20 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8299 (mm-30) REVERT: A 190 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8830 (tt0) REVERT: A 200 ASP cc_start: 0.7937 (t0) cc_final: 0.7674 (OUTLIER) REVERT: A 206 ASP cc_start: 0.8699 (t0) cc_final: 0.8337 (t0) REVERT: A 235 GLU cc_start: 0.8384 (tp30) cc_final: 0.7772 (tp30) REVERT: A 274 LYS cc_start: 0.9232 (pptt) cc_final: 0.9027 (pptt) REVERT: P 27 LYS cc_start: 0.9391 (mtmm) cc_final: 0.8874 (mmtt) REVERT: B 215 GLU cc_start: 0.8410 (pm20) cc_final: 0.8078 (pm20) REVERT: B 217 MET cc_start: 0.8100 (pmt) cc_final: 0.7820 (pmt) REVERT: B 228 ASP cc_start: 0.8211 (m-30) cc_final: 0.7656 (m-30) REVERT: B 260 GLU cc_start: 0.8332 (pt0) cc_final: 0.7766 (pm20) REVERT: B 262 MET cc_start: 0.8306 (pmm) cc_final: 0.7936 (ppp) REVERT: B 268 ASN cc_start: 0.8766 (m110) cc_final: 0.8535 (m110) REVERT: G 42 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8134 (mp0) REVERT: G 46 LYS cc_start: 0.8956 (ttpm) cc_final: 0.8732 (tppt) REVERT: G 50 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7777 (mm) REVERT: N 38 ARG cc_start: 0.8853 (ptt180) cc_final: 0.8555 (ptm-80) REVERT: N 80 TYR cc_start: 0.7916 (m-80) cc_final: 0.7583 (m-80) REVERT: N 89 GLU cc_start: 0.8484 (mp0) cc_final: 0.8229 (pm20) REVERT: R 204 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.5858 (pmt) REVERT: R 221 GLN cc_start: 0.8396 (mt0) cc_final: 0.7789 (mm110) REVERT: R 265 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7811 (tp) REVERT: R 340 MET cc_start: 0.8176 (ppp) cc_final: 0.7902 (ppp) REVERT: R 408 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8091 (mt-10) outliers start: 24 outliers final: 14 residues processed: 156 average time/residue: 0.6259 time to fit residues: 103.9057 Evaluate side-chains 155 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 190 GLN A 246 ASN N 77 ASN ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.113756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.078296 restraints weight = 16048.642| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.21 r_work: 0.2941 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9207 Z= 0.189 Angle : 0.599 9.859 12489 Z= 0.317 Chirality : 0.043 0.139 1406 Planarity : 0.004 0.040 1590 Dihedral : 6.882 82.147 1287 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.82 % Allowed : 22.97 % Favored : 74.21 % 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: 0.19 (0.25), residues: 1151 helix: 2.27 (0.26), residues: 439 sheet: -0.98 (0.31), residues: 239 loop : -1.35 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.020 0.002 TYR R 148 PHE 0.011 0.001 PHE R 230 TRP 0.015 0.001 TRP R 214 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 9201) covalent geometry : angle 0.59828 (12479) SS BOND : bond 0.00192 ( 5) SS BOND : angle 0.89331 ( 10) hydrogen bonds : bond 0.03750 ( 432) hydrogen bonds : angle 4.39225 ( 1239) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.378 Fit side-chains REVERT: A 20 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8313 (mm-30) REVERT: A 190 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8892 (tt0) REVERT: A 206 ASP cc_start: 0.8771 (t0) cc_final: 0.8405 (t0) REVERT: A 235 GLU cc_start: 0.8431 (tp30) cc_final: 0.7825 (tp30) REVERT: A 266 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8636 (mm-30) REVERT: A 274 LYS cc_start: 0.9263 (pptt) cc_final: 0.9057 (pptt) REVERT: P 27 LYS cc_start: 0.9379 (mtmm) cc_final: 0.8902 (mmtt) REVERT: B 215 GLU cc_start: 0.8287 (pm20) cc_final: 0.8012 (pm20) REVERT: B 217 MET cc_start: 0.8042 (pmt) cc_final: 0.7837 (pmt) REVERT: B 228 ASP cc_start: 0.8381 (m-30) cc_final: 0.7964 (m-30) REVERT: B 260 GLU cc_start: 0.8444 (pt0) cc_final: 0.7859 (pm20) REVERT: B 262 MET cc_start: 0.8335 (pmm) cc_final: 0.7571 (pmm) REVERT: B 268 ASN cc_start: 0.8773 (m110) cc_final: 0.8551 (m110) REVERT: G 42 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8124 (mp0) REVERT: G 46 LYS cc_start: 0.8936 (ttpm) cc_final: 0.8697 (tppt) REVERT: G 50 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7803 (mm) REVERT: N 38 ARG cc_start: 0.8898 (ptt180) cc_final: 0.8409 (ptm-80) REVERT: N 80 TYR cc_start: 0.7904 (m-80) cc_final: 0.7580 (m-80) REVERT: N 89 GLU cc_start: 0.8518 (mp0) cc_final: 0.8045 (pp20) REVERT: N 90 ASP cc_start: 0.7958 (m-30) cc_final: 0.7113 (m-30) REVERT: R 204 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.6292 (pmt) REVERT: R 265 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7835 (tp) REVERT: R 408 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8098 (mt-10) outliers start: 26 outliers final: 17 residues processed: 156 average time/residue: 0.6167 time to fit residues: 102.3763 Evaluate side-chains 159 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 84 optimal weight: 0.0030 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 246 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.114265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.078891 restraints weight = 15923.646| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.22 r_work: 0.2952 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9207 Z= 0.163 Angle : 0.597 10.145 12489 Z= 0.315 Chirality : 0.042 0.144 1406 Planarity : 0.004 0.040 1590 Dihedral : 6.820 80.752 1287 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.49 % Allowed : 23.51 % Favored : 74.00 % 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: 0.26 (0.25), residues: 1151 helix: 2.37 (0.26), residues: 433 sheet: -0.91 (0.32), residues: 237 loop : -1.33 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 284 TYR 0.019 0.002 TYR R 148 PHE 0.011 0.001 PHE R 324 TRP 0.018 0.001 TRP R 214 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9201) covalent geometry : angle 0.59674 (12479) SS BOND : bond 0.00182 ( 5) SS BOND : angle 0.85820 ( 10) hydrogen bonds : bond 0.03679 ( 432) hydrogen bonds : angle 4.40462 ( 1239) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.421 Fit side-chains REVERT: A 20 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8281 (mm-30) REVERT: A 190 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8854 (tt0) REVERT: A 206 ASP cc_start: 0.8777 (t0) cc_final: 0.8416 (t0) REVERT: A 235 GLU cc_start: 0.8453 (tp30) cc_final: 0.7828 (tp30) REVERT: A 274 LYS cc_start: 0.9274 (pptt) cc_final: 0.9072 (pptt) REVERT: P 27 LYS cc_start: 0.9388 (mtmm) cc_final: 0.8913 (mmtt) REVERT: B 228 ASP cc_start: 0.8403 (m-30) cc_final: 0.7872 (m-30) REVERT: B 260 GLU cc_start: 0.8453 (pt0) cc_final: 0.7849 (pm20) REVERT: B 262 MET cc_start: 0.8254 (pmm) cc_final: 0.7653 (pmm) REVERT: B 268 ASN cc_start: 0.8786 (m110) cc_final: 0.8543 (m110) REVERT: G 42 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8126 (mp0) REVERT: G 46 LYS cc_start: 0.8931 (ttpm) cc_final: 0.8694 (tppt) REVERT: G 50 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7808 (mm) REVERT: N 38 ARG cc_start: 0.8904 (ptt180) cc_final: 0.8433 (ptm-80) REVERT: N 80 TYR cc_start: 0.7866 (m-80) cc_final: 0.7544 (m-80) REVERT: N 87 LYS cc_start: 0.7547 (ttmm) cc_final: 0.6976 (ttmt) REVERT: N 89 GLU cc_start: 0.8479 (mp0) cc_final: 0.8086 (pp20) REVERT: N 90 ASP cc_start: 0.7900 (m-30) cc_final: 0.7075 (m-30) REVERT: R 204 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.6297 (pmt) REVERT: R 265 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7839 (tp) REVERT: R 408 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8095 (mt-10) outliers start: 23 outliers final: 15 residues processed: 156 average time/residue: 0.6226 time to fit residues: 103.5448 Evaluate side-chains 157 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 102 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 246 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.114519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.079154 restraints weight = 16032.274| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.23 r_work: 0.2931 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9207 Z= 0.160 Angle : 0.617 11.057 12489 Z= 0.323 Chirality : 0.043 0.194 1406 Planarity : 0.004 0.040 1590 Dihedral : 6.709 78.694 1287 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.60 % Allowed : 23.62 % Favored : 73.78 % 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: 0.30 (0.25), residues: 1151 helix: 2.38 (0.26), residues: 433 sheet: -0.87 (0.32), residues: 235 loop : -1.31 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 284 TYR 0.019 0.001 TYR R 148 PHE 0.013 0.001 PHE A 189 TRP 0.018 0.001 TRP R 214 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9201) covalent geometry : angle 0.61689 (12479) SS BOND : bond 0.00177 ( 5) SS BOND : angle 0.85131 ( 10) hydrogen bonds : bond 0.03661 ( 432) hydrogen bonds : angle 4.38702 ( 1239) Misc. bond : bond 0.00025 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.397 Fit side-chains REVERT: A 20 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8267 (mm-30) REVERT: A 190 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8835 (tt0) REVERT: A 200 ASP cc_start: 0.7964 (t0) cc_final: 0.7701 (t0) REVERT: A 206 ASP cc_start: 0.8782 (t0) cc_final: 0.8421 (t0) REVERT: A 235 GLU cc_start: 0.8447 (tp30) cc_final: 0.7752 (tp30) REVERT: A 274 LYS cc_start: 0.9283 (pptt) cc_final: 0.9070 (pptt) REVERT: P 27 LYS cc_start: 0.9376 (mtmm) cc_final: 0.8911 (mmtt) REVERT: B 215 GLU cc_start: 0.8606 (pm20) cc_final: 0.8083 (pm20) REVERT: B 217 MET cc_start: 0.8806 (pmm) cc_final: 0.8332 (pmm) REVERT: B 228 ASP cc_start: 0.8374 (m-30) cc_final: 0.7860 (m-30) REVERT: B 260 GLU cc_start: 0.8443 (pt0) cc_final: 0.7838 (pm20) REVERT: B 262 MET cc_start: 0.8092 (pmm) cc_final: 0.7717 (pmm) REVERT: B 268 ASN cc_start: 0.8788 (m110) cc_final: 0.8545 (m110) REVERT: G 46 LYS cc_start: 0.8916 (ttpm) cc_final: 0.8694 (tppt) REVERT: G 50 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7811 (mm) REVERT: G 62 ARG cc_start: 0.7454 (ppt170) cc_final: 0.6180 (mmt90) REVERT: N 38 ARG cc_start: 0.8862 (ptt180) cc_final: 0.8404 (ptm-80) REVERT: N 80 TYR cc_start: 0.7865 (m-80) cc_final: 0.7542 (m-80) REVERT: N 87 LYS cc_start: 0.7460 (ttmm) cc_final: 0.6873 (ttmt) REVERT: N 89 GLU cc_start: 0.8468 (mp0) cc_final: 0.8083 (pp20) REVERT: N 90 ASP cc_start: 0.7717 (m-30) cc_final: 0.6907 (m-30) REVERT: R 204 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.6419 (pmt) REVERT: R 265 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7813 (tp) REVERT: R 340 MET cc_start: 0.8165 (ppp) cc_final: 0.7852 (ppp) REVERT: R 408 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8094 (mt-10) outliers start: 24 outliers final: 16 residues processed: 158 average time/residue: 0.6334 time to fit residues: 106.6611 Evaluate side-chains 160 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 0.0980 chunk 78 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 11 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 246 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.115300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.080001 restraints weight = 15851.248| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.24 r_work: 0.2974 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9207 Z= 0.132 Angle : 0.607 11.410 12489 Z= 0.316 Chirality : 0.042 0.194 1406 Planarity : 0.004 0.040 1590 Dihedral : 6.506 75.474 1287 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.95 % Allowed : 24.27 % Favored : 73.78 % 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: 0.36 (0.25), residues: 1151 helix: 2.46 (0.26), residues: 432 sheet: -0.82 (0.32), residues: 235 loop : -1.31 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 284 TYR 0.018 0.001 TYR R 148 PHE 0.012 0.001 PHE A 189 TRP 0.017 0.001 TRP R 214 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9201) covalent geometry : angle 0.60648 (12479) SS BOND : bond 0.00164 ( 5) SS BOND : angle 0.77494 ( 10) hydrogen bonds : bond 0.03506 ( 432) hydrogen bonds : angle 4.33742 ( 1239) Misc. bond : bond 0.00016 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4036.85 seconds wall clock time: 69 minutes 33.86 seconds (4173.86 seconds total)