Starting phenix.real_space_refine on Wed Mar 4 10:53:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xbx_33108/03_2026/7xbx_33108.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xbx_33108/03_2026/7xbx_33108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xbx_33108/03_2026/7xbx_33108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xbx_33108/03_2026/7xbx_33108.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xbx_33108/03_2026/7xbx_33108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xbx_33108/03_2026/7xbx_33108.map" } resolution = 3.4 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 263 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 45 5.16 5 C 4260 2.51 5 N 1080 2.21 5 O 1231 1.98 5 H 6028 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12644 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3128 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 4, 'GLU:plan': 5, 'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 4293 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 305} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 13, 'GLU:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "E" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 414 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 4, 'TRANS': 28} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 4753 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 10, 'TRANS': 338} Chain breaks: 2 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PCA:plan-2': 1, 'HIS:plan': 6, 'GLN:plan1': 9, 'ASN:plan1': 3, 'ARG:plan': 5, 'GLU:plan': 7, 'ASP:plan': 5, 'TYR:plan': 4, 'PHE:plan': 10, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 241 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.17, per 1000 atoms: 0.17 Number of scatterers: 12644 At special positions: 0 Unit cell: (112.86, 131.67, 74.195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 O 1231 8.00 N 1080 7.00 C 4260 6.00 H 6028 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 8 " - pdb=" SG CYS R 34 " distance=2.03 Simple disulfide: pdb=" SG CYS R 12 " - pdb=" SG CYS R 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 35 " - pdb=" SG CYS R 278 " distance=2.03 Simple disulfide: pdb=" SG CYS R 204 " - pdb=" SG CYS R 277 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 418.8 milliseconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 43.9% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'C' and resid 6 through 32 Processing helix chain 'C' and resid 45 through 51 Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.830A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 216 No H-bonds generated for 'chain 'C' and resid 214 through 216' Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.876A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 311 removed outlier: 3.672A pdb=" N ASN C 311 " --> pdb=" O PHE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 348 removed outlier: 3.959A pdb=" N ASN C 331 " --> pdb=" O THR C 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 36 removed outlier: 4.307A pdb=" N ASN D 36 " --> pdb=" O ILE D 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 44 Processing helix chain 'R' and resid 29 through 34 removed outlier: 3.846A pdb=" N SER R 33 " --> pdb=" O GLN R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 66 removed outlier: 3.823A pdb=" N ASP R 60 " --> pdb=" O GLN R 56 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA R 61 " --> pdb=" O TRP R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 160 removed outlier: 3.504A pdb=" N PHE R 131 " --> pdb=" O ASP R 127 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE R 138 " --> pdb=" O VAL R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 196 Proline residue: R 187 - end of helix removed outlier: 3.516A pdb=" N ASN R 195 " --> pdb=" O HIS R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 235 Processing helix chain 'R' and resid 235 through 243 removed outlier: 4.148A pdb=" N MET R 240 " --> pdb=" O ALA R 236 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 269 Proline residue: R 265 - end of helix removed outlier: 4.490A pdb=" N PHE R 269 " --> pdb=" O PRO R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 286 removed outlier: 3.516A pdb=" N GLN R 286 " --> pdb=" O GLU R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 300 removed outlier: 3.515A pdb=" N VAL R 291 " --> pdb=" O GLU R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 323 Processing helix chain 'R' and resid 329 through 360 removed outlier: 3.558A pdb=" N ILE R 335 " --> pdb=" O ALA R 331 " (cutoff:3.500A) Proline residue: R 348 - end of helix removed outlier: 3.614A pdb=" N LEU R 360 " --> pdb=" O GLU R 356 " (cutoff:3.500A) Processing helix chain 'R' and resid 366 through 399 removed outlier: 3.671A pdb=" N CYS R 389 " --> pdb=" O PHE R 385 " (cutoff:3.500A) Proline residue: R 392 - end of helix Processing helix chain 'R' and resid 400 through 410 Processing sheet with id=AA1, first strand: chain 'C' and resid 185 through 191 removed outlier: 3.574A pdb=" N VAL C 185 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET C 198 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 38 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.527A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 61 through 63 removed outlier: 3.583A pdb=" N HIS D 62 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER D 72 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE D 80 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 103 through 105 removed outlier: 5.702A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 150 removed outlier: 3.663A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 187 through 192 removed outlier: 7.049A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE D 199 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP D 211 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N SER D 201 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS D 209 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA D 203 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.671A pdb=" N ALA D 231 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N THR D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.908A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 271 through 272 347 hydrogen bonds defined for protein. 1008 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: 2.56 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6000 1.04 - 1.23: 180 1.23 - 1.43: 2662 1.43 - 1.63: 3884 1.63 - 1.83: 56 Bond restraints: 12782 Sorted by residual: bond pdb=" C5 CLR R 501 " pdb=" C6 CLR R 501 " ideal model delta sigma weight residual 1.332 1.463 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" C5 CLR R 502 " pdb=" C6 CLR R 502 " ideal model delta sigma weight residual 1.332 1.463 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" N PCA R 1 " pdb=" CD PCA R 1 " ideal model delta sigma weight residual 1.345 1.465 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C3 CLR R 502 " pdb=" O1 CLR R 502 " ideal model delta sigma weight residual 1.413 1.300 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C3 CLR R 501 " pdb=" O1 CLR R 501 " ideal model delta sigma weight residual 1.413 1.300 0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 12777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.14: 22925 9.14 - 18.28: 1 18.28 - 27.43: 0 27.43 - 36.57: 0 36.57 - 45.71: 1 Bond angle restraints: 22927 Sorted by residual: angle pdb=" CD PCA R 1 " pdb=" N PCA R 1 " pdb=" H PCA R 1 " ideal model delta sigma weight residual 120.30 74.59 45.71 3.00e+00 1.11e-01 2.32e+02 angle pdb=" CA PCA R 1 " pdb=" N PCA R 1 " pdb=" CD PCA R 1 " ideal model delta sigma weight residual 114.17 103.35 10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" N PCA R 1 " pdb=" CD PCA R 1 " pdb=" CG PCA R 1 " ideal model delta sigma weight residual 107.23 114.76 -7.53 3.00e+00 1.11e-01 6.30e+00 angle pdb=" CA CYS R 277 " pdb=" CB CYS R 277 " pdb=" SG CYS R 277 " ideal model delta sigma weight residual 114.40 120.10 -5.70 2.30e+00 1.89e-01 6.15e+00 angle pdb=" CB ARG R 293 " pdb=" CG ARG R 293 " pdb=" CD ARG R 293 " ideal model delta sigma weight residual 111.30 116.00 -4.70 2.30e+00 1.89e-01 4.18e+00 ... (remaining 22922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 5682 15.67 - 31.34: 410 31.34 - 47.01: 122 47.01 - 62.67: 51 62.67 - 78.34: 3 Dihedral angle restraints: 6268 sinusoidal: 3147 harmonic: 3121 Sorted by residual: dihedral pdb=" CB CYS R 204 " pdb=" SG CYS R 204 " pdb=" SG CYS R 277 " pdb=" CB CYS R 277 " ideal model delta sinusoidal sigma weight residual -86.00 -128.07 42.07 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA CYS R 8 " pdb=" CB CYS R 8 " pdb=" SG CYS R 8 " pdb=" SG CYS R 34 " ideal model delta sinusoidal sigma weight residual -73.00 2.56 -75.56 1 2.00e+01 2.50e-03 1.80e+01 dihedral pdb=" SG CYS R 204 " pdb=" CB CYS R 277 " pdb=" SG CYS R 277 " pdb=" CA CYS R 277 " ideal model delta sinusoidal sigma weight residual -73.00 -13.85 -59.15 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 6265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 951 0.047 - 0.094: 137 0.094 - 0.141: 48 0.141 - 0.188: 3 0.188 - 0.235: 2 Chirality restraints: 1141 Sorted by residual: chirality pdb=" C14 CLR R 501 " pdb=" C13 CLR R 501 " pdb=" C15 CLR R 501 " pdb=" C8 CLR R 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C14 CLR R 502 " pdb=" C13 CLR R 502 " pdb=" C15 CLR R 502 " pdb=" C8 CLR R 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C3 CLR R 502 " pdb=" C2 CLR R 502 " pdb=" C4 CLR R 502 " pdb=" O1 CLR R 502 " both_signs ideal model delta sigma weight residual False -2.46 -2.29 -0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 1138 not shown) Planarity restraints: 2035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N PCA R 1 " 0.289 2.00e-02 2.50e+03 2.69e-01 1.08e+03 pdb=" CA PCA R 1 " 0.142 2.00e-02 2.50e+03 pdb=" CG PCA R 1 " -0.174 2.00e-02 2.50e+03 pdb=" CD PCA R 1 " 0.105 2.00e-02 2.50e+03 pdb=" OE PCA R 1 " 0.152 2.00e-02 2.50e+03 pdb=" H PCA R 1 " -0.514 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 287 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO C 288 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 288 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 288 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 189 " -0.004 2.00e-02 2.50e+03 6.77e-03 1.83e+00 pdb=" CG TRP R 189 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP R 189 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP R 189 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 189 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP R 189 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 189 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 189 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 189 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 189 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP R 189 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP R 189 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP R 189 " 0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP R 189 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP R 189 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP R 189 " 0.000 2.00e-02 2.50e+03 ... (remaining 2032 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 648 2.19 - 2.79: 25019 2.79 - 3.40: 34276 3.40 - 4.00: 43591 4.00 - 4.60: 67214 Nonbonded interactions: 170748 Sorted by model distance: nonbonded pdb=" O ASN D 230 " pdb="HD21 ASN D 230 " model vdw 1.588 2.450 nonbonded pdb=" O ARG D 314 " pdb=" H TRP D 332 " model vdw 1.662 2.450 nonbonded pdb=" O GLY D 77 " pdb=" H LEU D 95 " model vdw 1.691 2.450 nonbonded pdb=" O PHE R 343 " pdb=" HG1 THR R 347 " model vdw 1.692 2.450 nonbonded pdb=" O GLY D 144 " pdb=" HG SER D 161 " model vdw 1.710 2.450 ... (remaining 170743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.080 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.640 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 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 : 0.004 0.131 6758 Z= 0.217 Angle : 0.516 10.822 9260 Z= 0.251 Chirality : 0.040 0.235 1141 Planarity : 0.002 0.042 1155 Dihedral : 12.584 78.343 2283 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.30), residues: 892 helix: 2.88 (0.28), residues: 363 sheet: -0.18 (0.44), residues: 152 loop : -0.65 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG R 293 TYR 0.009 0.001 TYR R 140 PHE 0.015 0.001 PHE R 211 TRP 0.021 0.001 TRP R 189 HIS 0.011 0.001 HIS R 2 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 6754) covalent geometry : angle 0.51329 ( 9252) SS BOND : bond 0.00299 ( 4) SS BOND : angle 1.77243 ( 8) hydrogen bonds : bond 0.18979 ( 347) hydrogen bonds : angle 6.64471 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 183 VAL cc_start: 0.7704 (t) cc_final: 0.7325 (p) REVERT: R 337 LEU cc_start: 0.7992 (mp) cc_final: 0.7781 (mp) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.1356 time to fit residues: 32.3266 Evaluate side-chains 131 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN D 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.183832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.147764 restraints weight = 24617.549| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 3.12 r_work: 0.4021 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6758 Z= 0.129 Angle : 0.493 4.818 9260 Z= 0.266 Chirality : 0.038 0.165 1141 Planarity : 0.003 0.037 1155 Dihedral : 3.348 21.893 1074 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.09 % Allowed : 10.92 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.29), residues: 892 helix: 2.59 (0.27), residues: 369 sheet: -0.12 (0.45), residues: 142 loop : -0.85 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 293 TYR 0.011 0.001 TYR D 105 PHE 0.017 0.001 PHE C 307 TRP 0.009 0.001 TRP D 297 HIS 0.009 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6754) covalent geometry : angle 0.49090 ( 9252) SS BOND : bond 0.00560 ( 4) SS BOND : angle 1.49988 ( 8) hydrogen bonds : bond 0.04161 ( 347) hydrogen bonds : angle 4.93351 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 TYR cc_start: 0.7018 (t80) cc_final: 0.6151 (t80) REVERT: R 183 VAL cc_start: 0.7502 (t) cc_final: 0.7164 (p) REVERT: R 302 PHE cc_start: 0.7037 (t80) cc_final: 0.6779 (t80) outliers start: 7 outliers final: 4 residues processed: 148 average time/residue: 0.1356 time to fit residues: 28.1647 Evaluate side-chains 135 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 ASN R 325 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.174310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.136558 restraints weight = 25330.790| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 3.10 r_work: 0.3848 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6758 Z= 0.174 Angle : 0.506 5.689 9260 Z= 0.278 Chirality : 0.038 0.149 1141 Planarity : 0.003 0.040 1155 Dihedral : 3.760 22.067 1074 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.18 % Allowed : 14.82 % Favored : 83.00 % 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 are not related in a simple way. whole: 0.63 (0.29), residues: 892 helix: 2.46 (0.27), residues: 369 sheet: -1.14 (0.44), residues: 140 loop : -1.04 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 293 TYR 0.014 0.001 TYR R 313 PHE 0.015 0.002 PHE C 196 TRP 0.011 0.001 TRP D 297 HIS 0.007 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6754) covalent geometry : angle 0.50455 ( 9252) SS BOND : bond 0.01041 ( 4) SS BOND : angle 1.45527 ( 8) hydrogen bonds : bond 0.04081 ( 347) hydrogen bonds : angle 4.74502 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 MET cc_start: 0.6839 (tpt) cc_final: 0.6597 (tpt) REVERT: C 297 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8070 (mp0) REVERT: D 196 THR cc_start: 0.6548 (p) cc_final: 0.6293 (p) outliers start: 14 outliers final: 9 residues processed: 151 average time/residue: 0.1302 time to fit residues: 27.7178 Evaluate side-chains 134 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 238 ASN Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 316 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 295 ASN R 350 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.173671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.137533 restraints weight = 24540.095| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.96 r_work: 0.3888 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6758 Z= 0.139 Angle : 0.476 4.886 9260 Z= 0.260 Chirality : 0.038 0.156 1141 Planarity : 0.003 0.040 1155 Dihedral : 3.557 20.225 1074 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.50 % Allowed : 15.76 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.29), residues: 892 helix: 2.53 (0.27), residues: 369 sheet: -1.22 (0.42), residues: 150 loop : -1.05 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 208 TYR 0.011 0.001 TYR R 313 PHE 0.013 0.001 PHE C 196 TRP 0.013 0.001 TRP D 99 HIS 0.005 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6754) covalent geometry : angle 0.47488 ( 9252) SS BOND : bond 0.00148 ( 4) SS BOND : angle 1.20979 ( 8) hydrogen bonds : bond 0.03727 ( 347) hydrogen bonds : angle 4.65519 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 297 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8086 (mp0) REVERT: D 105 TYR cc_start: 0.7475 (t80) cc_final: 0.6365 (t80) REVERT: D 196 THR cc_start: 0.6503 (p) cc_final: 0.6225 (p) REVERT: D 210 LEU cc_start: 0.7772 (tp) cc_final: 0.7507 (tp) outliers start: 16 outliers final: 11 residues processed: 151 average time/residue: 0.1288 time to fit residues: 27.4941 Evaluate side-chains 144 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 238 ASN Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 367 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.172023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.134751 restraints weight = 25241.006| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.04 r_work: 0.3816 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6758 Z= 0.150 Angle : 0.476 4.637 9260 Z= 0.260 Chirality : 0.038 0.145 1141 Planarity : 0.003 0.040 1155 Dihedral : 3.588 22.181 1074 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.65 % Allowed : 17.32 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.29), residues: 892 helix: 2.56 (0.27), residues: 368 sheet: -1.22 (0.41), residues: 154 loop : -1.10 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 208 TYR 0.011 0.001 TYR R 313 PHE 0.012 0.001 PHE C 196 TRP 0.014 0.001 TRP D 99 HIS 0.005 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6754) covalent geometry : angle 0.47578 ( 9252) SS BOND : bond 0.00168 ( 4) SS BOND : angle 1.00197 ( 8) hydrogen bonds : bond 0.03705 ( 347) hydrogen bonds : angle 4.62865 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 297 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8185 (mp0) REVERT: D 76 ASP cc_start: 0.7181 (t70) cc_final: 0.6977 (t0) REVERT: D 93 ILE cc_start: 0.8150 (pt) cc_final: 0.7939 (pt) REVERT: D 105 TYR cc_start: 0.7663 (t80) cc_final: 0.6501 (t80) REVERT: D 196 THR cc_start: 0.6618 (p) cc_final: 0.6330 (p) outliers start: 17 outliers final: 13 residues processed: 146 average time/residue: 0.1293 time to fit residues: 26.4037 Evaluate side-chains 146 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 238 ASN Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 367 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 ASN D 259 GLN R 350 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.171162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.134309 restraints weight = 25267.192| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.95 r_work: 0.3813 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6758 Z= 0.133 Angle : 0.466 4.284 9260 Z= 0.253 Chirality : 0.038 0.141 1141 Planarity : 0.003 0.041 1155 Dihedral : 3.530 22.383 1074 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.81 % Allowed : 17.47 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.29), residues: 892 helix: 2.61 (0.27), residues: 370 sheet: -1.13 (0.42), residues: 146 loop : -1.10 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 314 TYR 0.011 0.001 TYR R 349 PHE 0.010 0.001 PHE C 196 TRP 0.010 0.001 TRP D 99 HIS 0.005 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6754) covalent geometry : angle 0.46553 ( 9252) SS BOND : bond 0.00324 ( 4) SS BOND : angle 1.01500 ( 8) hydrogen bonds : bond 0.03608 ( 347) hydrogen bonds : angle 4.53638 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 GLU cc_start: 0.7301 (tt0) cc_final: 0.7092 (tt0) REVERT: C 297 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8258 (mp0) REVERT: D 76 ASP cc_start: 0.7206 (t70) cc_final: 0.6955 (t0) REVERT: D 105 TYR cc_start: 0.7836 (t80) cc_final: 0.6802 (t80) REVERT: D 196 THR cc_start: 0.6708 (p) cc_final: 0.6414 (p) outliers start: 18 outliers final: 15 residues processed: 159 average time/residue: 0.1262 time to fit residues: 28.9916 Evaluate side-chains 151 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 212 PHE Chi-restraints excluded: chain R residue 238 ASN Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 367 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 77 optimal weight: 0.0040 chunk 15 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.172762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.135681 restraints weight = 25242.151| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.98 r_work: 0.3831 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6758 Z= 0.111 Angle : 0.455 4.255 9260 Z= 0.246 Chirality : 0.037 0.150 1141 Planarity : 0.003 0.039 1155 Dihedral : 3.853 57.213 1074 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.50 % Allowed : 19.03 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.30), residues: 892 helix: 2.69 (0.27), residues: 369 sheet: -1.14 (0.42), residues: 146 loop : -1.09 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 314 TYR 0.012 0.001 TYR R 349 PHE 0.010 0.001 PHE C 196 TRP 0.015 0.001 TRP D 99 HIS 0.005 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 6754) covalent geometry : angle 0.45415 ( 9252) SS BOND : bond 0.00400 ( 4) SS BOND : angle 1.10239 ( 8) hydrogen bonds : bond 0.03479 ( 347) hydrogen bonds : angle 4.41825 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 297 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8232 (mp0) REVERT: D 76 ASP cc_start: 0.7240 (t70) cc_final: 0.7009 (t0) REVERT: D 105 TYR cc_start: 0.7733 (t80) cc_final: 0.6804 (t80) REVERT: D 196 THR cc_start: 0.6649 (p) cc_final: 0.6359 (p) outliers start: 16 outliers final: 13 residues processed: 154 average time/residue: 0.1120 time to fit residues: 25.6493 Evaluate side-chains 150 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 367 CYS Chi-restraints excluded: chain R residue 408 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.171530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.134576 restraints weight = 25072.294| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.93 r_work: 0.3820 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6758 Z= 0.124 Angle : 0.466 4.165 9260 Z= 0.254 Chirality : 0.038 0.150 1141 Planarity : 0.003 0.039 1155 Dihedral : 3.909 59.397 1074 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.50 % Allowed : 20.12 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.30), residues: 892 helix: 2.65 (0.27), residues: 369 sheet: -1.22 (0.42), residues: 146 loop : -1.13 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 314 TYR 0.012 0.001 TYR R 349 PHE 0.010 0.001 PHE C 196 TRP 0.023 0.002 TRP D 63 HIS 0.005 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6754) covalent geometry : angle 0.46500 ( 9252) SS BOND : bond 0.00254 ( 4) SS BOND : angle 1.18506 ( 8) hydrogen bonds : bond 0.03512 ( 347) hydrogen bonds : angle 4.45694 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 308 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7448 (mm-30) REVERT: D 76 ASP cc_start: 0.7342 (t70) cc_final: 0.7124 (t0) REVERT: D 105 TYR cc_start: 0.7787 (t80) cc_final: 0.6948 (t80) outliers start: 16 outliers final: 16 residues processed: 150 average time/residue: 0.1187 time to fit residues: 26.4575 Evaluate side-chains 153 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 212 PHE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 367 CYS Chi-restraints excluded: chain R residue 408 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 73 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 69 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN R 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.165766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.127954 restraints weight = 25631.473| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 3.01 r_work: 0.3714 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6758 Z= 0.194 Angle : 0.522 4.397 9260 Z= 0.289 Chirality : 0.039 0.147 1141 Planarity : 0.004 0.041 1155 Dihedral : 4.456 58.723 1074 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.96 % Allowed : 19.50 % Favored : 77.54 % 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 are not related in a simple way. whole: 0.29 (0.29), residues: 892 helix: 2.30 (0.27), residues: 374 sheet: -1.52 (0.39), residues: 157 loop : -1.29 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 314 TYR 0.012 0.002 TYR D 105 PHE 0.012 0.002 PHE C 196 TRP 0.019 0.002 TRP D 99 HIS 0.005 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 6754) covalent geometry : angle 0.52073 ( 9252) SS BOND : bond 0.00174 ( 4) SS BOND : angle 1.17187 ( 8) hydrogen bonds : bond 0.03908 ( 347) hydrogen bonds : angle 4.79339 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 17 residues processed: 159 average time/residue: 0.1187 time to fit residues: 27.7103 Evaluate side-chains 151 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 212 PHE Chi-restraints excluded: chain R residue 238 ASN Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 367 CYS Chi-restraints excluded: chain R residue 408 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.167403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.129608 restraints weight = 25563.116| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.07 r_work: 0.3761 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6758 Z= 0.123 Angle : 0.486 4.343 9260 Z= 0.264 Chirality : 0.038 0.152 1141 Planarity : 0.003 0.040 1155 Dihedral : 3.979 42.518 1074 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.50 % Allowed : 20.90 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.29), residues: 892 helix: 2.47 (0.27), residues: 375 sheet: -1.57 (0.41), residues: 146 loop : -1.15 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 314 TYR 0.013 0.001 TYR R 349 PHE 0.012 0.001 PHE C 307 TRP 0.018 0.001 TRP D 63 HIS 0.005 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6754) covalent geometry : angle 0.48503 ( 9252) SS BOND : bond 0.00301 ( 4) SS BOND : angle 1.06476 ( 8) hydrogen bonds : bond 0.03576 ( 347) hydrogen bonds : angle 4.54763 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue TYR 287 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue MET 15 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue SER 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 59 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue TYR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 203 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue MET 268 is missing expected H atoms. Skipping. Residue LYS 271 is missing expected H atoms. Skipping. Residue TYR 281 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LYS 327 is missing expected H atoms. Skipping. Residue LEU 358 is missing expected H atoms. Skipping. Residue LYS 359 is missing expected H atoms. Skipping. Residue LEU 360 is missing expected H atoms. Skipping. Residue TYR 361 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 386 is missing expected H atoms. Skipping. Residue LEU 390 is missing expected H atoms. Skipping. Residue LEU 393 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 16 residues processed: 153 average time/residue: 0.1214 time to fit residues: 27.1611 Evaluate side-chains 153 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 212 PHE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 367 CYS Chi-restraints excluded: chain R residue 408 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.166155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.128690 restraints weight = 25833.861| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.00 r_work: 0.3730 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6758 Z= 0.169 Angle : 0.510 4.230 9260 Z= 0.280 Chirality : 0.038 0.153 1141 Planarity : 0.004 0.040 1155 Dihedral : 4.081 31.046 1074 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.34 % Allowed : 21.37 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.29), residues: 892 helix: 2.34 (0.27), residues: 375 sheet: -1.62 (0.39), residues: 157 loop : -1.20 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 314 TYR 0.012 0.002 TYR R 395 PHE 0.010 0.001 PHE R 212 TRP 0.026 0.002 TRP D 63 HIS 0.005 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6754) covalent geometry : angle 0.50913 ( 9252) SS BOND : bond 0.00162 ( 4) SS BOND : angle 1.08764 ( 8) hydrogen bonds : bond 0.03745 ( 347) hydrogen bonds : angle 4.69253 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3816.57 seconds wall clock time: 65 minutes 11.44 seconds (3911.44 seconds total)