Starting phenix.real_space_refine on Thu Jul 31 02:59:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xbx_33108/07_2025/7xbx_33108.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xbx_33108/07_2025/7xbx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xbx_33108/07_2025/7xbx_33108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xbx_33108/07_2025/7xbx_33108.map" model { file = "/net/cci-nas-00/data/ceres_data/7xbx_33108/07_2025/7xbx_33108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xbx_33108/07_2025/7xbx_33108.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} 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, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 13} 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: {'GLN:plan1': 9, 'ASP:plan': 5, 'PCA:plan-2': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 6, 'TYR:plan': 4, 'PHE:plan': 10, 'GLU:plan': 7, 'ARG:plan': 5} 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: 6.86, per 1000 atoms: 0.54 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: 4.02 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.99 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: 4.45 Time building geometry restraints manager: 4.06 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.230 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.770 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- 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 : 6.35 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.001 TRP R 189 HIS 0.011 0.001 HIS R 2 PHE 0.015 0.001 PHE R 211 TYR 0.009 0.001 TYR R 140 ARG 0.021 0.001 ARG R 293 Details of bonding type rmsd hydrogen bonds : bond 0.18979 ( 347) hydrogen bonds : angle 6.64471 ( 1008) SS BOND : bond 0.00299 ( 4) SS BOND : angle 1.77243 ( 8) covalent geometry : bond 0.00436 ( 6754) covalent geometry : angle 0.51329 ( 9252) *********************** 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 : 1.033 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: R 183 VAL cc_start: 0.7704 (t) cc_final: 0.7324 (p) REVERT: R 337 LEU cc_start: 0.7992 (mp) cc_final: 0.7780 (mp) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.3235 time to fit residues: 77.4703 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 : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 0.1980 chunk 80 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.183846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.147785 restraints weight = 24446.174| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 3.12 r_work: 0.4021 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6758 Z= 0.130 Angle : 0.493 5.029 9260 Z= 0.267 Chirality : 0.038 0.174 1141 Planarity : 0.003 0.037 1155 Dihedral : 3.332 22.554 1074 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.25 % Allowed : 10.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.29), residues: 892 helix: 2.57 (0.27), residues: 369 sheet: -0.14 (0.45), residues: 142 loop : -0.85 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 297 HIS 0.009 0.001 HIS C 322 PHE 0.016 0.001 PHE R 343 TYR 0.011 0.001 TYR D 105 ARG 0.004 0.001 ARG R 293 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 347) hydrogen bonds : angle 4.94233 ( 1008) SS BOND : bond 0.00205 ( 4) SS BOND : angle 1.46192 ( 8) covalent geometry : bond 0.00279 ( 6754) covalent geometry : angle 0.49153 ( 9252) *********************** 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 152 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 TYR cc_start: 0.7019 (t80) cc_final: 0.6169 (t80) REVERT: R 183 VAL cc_start: 0.7538 (t) cc_final: 0.7197 (p) outliers start: 8 outliers final: 4 residues processed: 150 average time/residue: 0.3158 time to fit residues: 66.5716 Evaluate side-chains 138 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 69 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 HIS D 230 ASN R 325 ASN R 350 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.170425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.132287 restraints weight = 25476.119| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.07 r_work: 0.3778 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6758 Z= 0.223 Angle : 0.554 5.426 9260 Z= 0.307 Chirality : 0.040 0.149 1141 Planarity : 0.004 0.042 1155 Dihedral : 4.243 29.719 1074 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.12 % Allowed : 14.82 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.28), residues: 892 helix: 2.09 (0.27), residues: 374 sheet: -1.41 (0.44), residues: 133 loop : -1.27 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 297 HIS 0.008 0.002 HIS D 54 PHE 0.015 0.002 PHE C 196 TYR 0.018 0.002 TYR D 105 ARG 0.003 0.001 ARG D 304 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 347) hydrogen bonds : angle 4.96089 ( 1008) SS BOND : bond 0.00757 ( 4) SS BOND : angle 1.52127 ( 8) covalent geometry : bond 0.00483 ( 6754) covalent geometry : angle 0.55254 ( 9252) *********************** 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 168 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.049 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: 0.8524 (mm-30) cc_final: 0.8093 (mp0) REVERT: C 311 ASN cc_start: 0.8754 (t0) cc_final: 0.8485 (t0) REVERT: D 93 ILE cc_start: 0.8225 (pt) cc_final: 0.7968 (pt) REVERT: D 196 THR cc_start: 0.6834 (p) cc_final: 0.6562 (p) REVERT: D 247 ASP cc_start: 0.7568 (m-30) cc_final: 0.7255 (t0) outliers start: 20 outliers final: 12 residues processed: 161 average time/residue: 0.3108 time to fit residues: 70.0296 Evaluate side-chains 146 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 D residue 179 THR Chi-restraints excluded: chain D residue 199 PHE 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 Chi-restraints excluded: chain R residue 367 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 55 optimal weight: 0.0370 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN D 230 ASN D 295 ASN ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.171535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.133730 restraints weight = 25136.397| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 3.08 r_work: 0.3810 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6758 Z= 0.144 Angle : 0.489 4.829 9260 Z= 0.265 Chirality : 0.038 0.151 1141 Planarity : 0.003 0.041 1155 Dihedral : 3.742 25.168 1074 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.34 % Allowed : 17.00 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.29), residues: 892 helix: 2.42 (0.27), residues: 368 sheet: -1.53 (0.43), residues: 133 loop : -1.06 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 99 HIS 0.006 0.001 HIS C 322 PHE 0.012 0.001 PHE C 189 TYR 0.012 0.001 TYR R 313 ARG 0.004 0.001 ARG D 304 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 347) hydrogen bonds : angle 4.73566 ( 1008) SS BOND : bond 0.00349 ( 4) SS BOND : angle 1.19008 ( 8) covalent geometry : bond 0.00310 ( 6754) covalent geometry : angle 0.48797 ( 9252) *********************** 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 162 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.963 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 297 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8113 (mp0) REVERT: D 105 TYR cc_start: 0.7765 (t80) cc_final: 0.6687 (t80) REVERT: D 196 THR cc_start: 0.6706 (p) cc_final: 0.6421 (p) REVERT: D 247 ASP cc_start: 0.7298 (m-30) cc_final: 0.7052 (t0) outliers start: 15 outliers final: 10 residues processed: 158 average time/residue: 0.3131 time to fit residues: 69.2682 Evaluate side-chains 145 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 316 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 48 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN D 230 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.168752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.130685 restraints weight = 25387.379| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.02 r_work: 0.3792 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6758 Z= 0.184 Angle : 0.507 4.340 9260 Z= 0.278 Chirality : 0.038 0.141 1141 Planarity : 0.004 0.043 1155 Dihedral : 3.931 29.088 1074 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.50 % Allowed : 18.41 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.29), residues: 892 helix: 2.28 (0.27), residues: 369 sheet: -1.46 (0.42), residues: 144 loop : -1.15 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 99 HIS 0.005 0.001 HIS C 322 PHE 0.012 0.001 PHE C 196 TYR 0.010 0.001 TYR D 105 ARG 0.005 0.000 ARG D 314 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 347) hydrogen bonds : angle 4.87684 ( 1008) SS BOND : bond 0.00105 ( 4) SS BOND : angle 1.11347 ( 8) covalent geometry : bond 0.00398 ( 6754) covalent geometry : angle 0.50633 ( 9252) *********************** 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 158 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.256 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: symmetry clash revert: symmetry clash REVERT: C 33 GLU cc_start: 0.7377 (tt0) cc_final: 0.7171 (tt0) REVERT: C 297 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8184 (mp0) REVERT: D 105 TYR cc_start: 0.7826 (t80) cc_final: 0.6811 (t80) REVERT: D 196 THR cc_start: 0.6766 (p) cc_final: 0.6462 (p) REVERT: D 247 ASP cc_start: 0.7440 (m-30) cc_final: 0.7204 (t0) outliers start: 16 outliers final: 14 residues processed: 154 average time/residue: 0.3561 time to fit residues: 76.1640 Evaluate side-chains 150 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 306 GLN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 243 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 81 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.169439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.131143 restraints weight = 25499.683| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.05 r_work: 0.3755 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6758 Z= 0.141 Angle : 0.482 4.163 9260 Z= 0.262 Chirality : 0.038 0.136 1141 Planarity : 0.003 0.039 1155 Dihedral : 3.778 27.771 1074 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.28 % Allowed : 19.03 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.29), residues: 892 helix: 2.34 (0.27), residues: 369 sheet: -1.29 (0.41), residues: 150 loop : -1.15 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 99 HIS 0.005 0.001 HIS C 322 PHE 0.011 0.001 PHE R 212 TYR 0.010 0.001 TYR R 313 ARG 0.003 0.000 ARG D 314 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 347) hydrogen bonds : angle 4.71327 ( 1008) SS BOND : bond 0.00090 ( 4) SS BOND : angle 1.13391 ( 8) covalent geometry : bond 0.00304 ( 6754) covalent geometry : angle 0.48106 ( 9252) *********************** 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 166 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.954 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 297 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8247 (mp0) REVERT: D 105 TYR cc_start: 0.7819 (t80) cc_final: 0.6834 (t80) REVERT: D 196 THR cc_start: 0.6741 (p) cc_final: 0.6451 (p) REVERT: D 247 ASP cc_start: 0.7279 (m-30) cc_final: 0.6918 (t0) outliers start: 21 outliers final: 16 residues processed: 160 average time/residue: 0.3076 time to fit residues: 70.7455 Evaluate side-chains 152 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 306 GLN Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 226 GLU 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 65 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 31 optimal weight: 0.0030 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 overall best weight: 0.7390 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.170351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.132611 restraints weight = 25368.949| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.04 r_work: 0.3783 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6758 Z= 0.122 Angle : 0.480 4.175 9260 Z= 0.260 Chirality : 0.038 0.138 1141 Planarity : 0.003 0.039 1155 Dihedral : 4.043 49.547 1074 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.65 % Allowed : 20.90 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.29), residues: 892 helix: 2.45 (0.27), residues: 369 sheet: -1.27 (0.42), residues: 139 loop : -1.09 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 63 HIS 0.005 0.001 HIS C 322 PHE 0.012 0.001 PHE R 342 TYR 0.010 0.001 TYR R 313 ARG 0.004 0.000 ARG D 314 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 347) hydrogen bonds : angle 4.63533 ( 1008) SS BOND : bond 0.00173 ( 4) SS BOND : angle 1.12690 ( 8) covalent geometry : bond 0.00269 ( 6754) covalent geometry : angle 0.47894 ( 9252) *********************** 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 157 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.947 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: D 105 TYR cc_start: 0.7779 (t80) cc_final: 0.6889 (t80) REVERT: D 196 THR cc_start: 0.6681 (p) cc_final: 0.6370 (p) REVERT: D 314 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6824 (ttp80) outliers start: 17 outliers final: 15 residues processed: 154 average time/residue: 0.2864 time to fit residues: 62.7084 Evaluate side-chains 148 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 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 D residue 314 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 74 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.169482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.131438 restraints weight = 25523.289| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.09 r_work: 0.3765 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6758 Z= 0.131 Angle : 0.482 4.130 9260 Z= 0.263 Chirality : 0.038 0.137 1141 Planarity : 0.003 0.038 1155 Dihedral : 4.074 45.955 1074 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.81 % Allowed : 21.37 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.29), residues: 892 helix: 2.48 (0.27), residues: 369 sheet: -1.26 (0.41), residues: 144 loop : -1.17 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 63 HIS 0.005 0.001 HIS C 322 PHE 0.012 0.001 PHE R 342 TYR 0.009 0.001 TYR R 313 ARG 0.005 0.000 ARG D 314 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 347) hydrogen bonds : angle 4.58003 ( 1008) SS BOND : bond 0.00259 ( 4) SS BOND : angle 1.06985 ( 8) covalent geometry : bond 0.00283 ( 6754) covalent geometry : angle 0.48087 ( 9252) *********************** 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 157 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 1.039 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: symmetry clash REVERT: C 33 GLU cc_start: 0.7252 (tt0) cc_final: 0.7032 (tt0) REVERT: C 333 GLN cc_start: 0.8396 (tp40) cc_final: 0.8029 (tp40) REVERT: D 196 THR cc_start: 0.6705 (p) cc_final: 0.6416 (p) REVERT: D 314 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6731 (ttp80) REVERT: R 189 TRP cc_start: 0.6763 (m100) cc_final: 0.6513 (m100) outliers start: 18 outliers final: 17 residues processed: 154 average time/residue: 0.3108 time to fit residues: 69.4287 Evaluate side-chains 151 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 306 GLN Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 226 GLU 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 D residue 314 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 81 optimal weight: 4.9990 chunk 75 optimal weight: 0.0970 chunk 4 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 55 optimal weight: 0.0370 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.171734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.133984 restraints weight = 25168.115| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 3.09 r_work: 0.3846 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6758 Z= 0.105 Angle : 0.476 4.172 9260 Z= 0.256 Chirality : 0.037 0.141 1141 Planarity : 0.003 0.038 1155 Dihedral : 3.913 45.263 1074 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.65 % Allowed : 21.84 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.30), residues: 892 helix: 2.61 (0.27), residues: 368 sheet: -1.27 (0.41), residues: 145 loop : -1.03 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 63 HIS 0.005 0.001 HIS C 322 PHE 0.010 0.001 PHE R 342 TYR 0.012 0.001 TYR R 395 ARG 0.004 0.000 ARG D 314 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 347) hydrogen bonds : angle 4.48023 ( 1008) SS BOND : bond 0.00211 ( 4) SS BOND : angle 1.07267 ( 8) covalent geometry : bond 0.00225 ( 6754) covalent geometry : angle 0.47485 ( 9252) *********************** 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 159 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.651 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: C 33 GLU cc_start: 0.7305 (tt0) cc_final: 0.7097 (tt0) REVERT: C 333 GLN cc_start: 0.8437 (tp40) cc_final: 0.8119 (tp40) REVERT: D 105 TYR cc_start: 0.7812 (t80) cc_final: 0.7021 (t80) REVERT: D 314 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6603 (ttp80) REVERT: R 189 TRP cc_start: 0.6597 (m100) cc_final: 0.6387 (m100) outliers start: 17 outliers final: 16 residues processed: 155 average time/residue: 0.3473 time to fit residues: 78.2481 Evaluate side-chains 152 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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 D residue 314 ARG 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 32 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.170478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.132621 restraints weight = 25355.505| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 3.07 r_work: 0.3857 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6758 Z= 0.117 Angle : 0.479 4.148 9260 Z= 0.259 Chirality : 0.037 0.141 1141 Planarity : 0.003 0.038 1155 Dihedral : 3.948 53.192 1074 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.81 % Allowed : 21.68 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.29), residues: 892 helix: 2.55 (0.27), residues: 375 sheet: -1.27 (0.40), residues: 149 loop : -0.98 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 63 HIS 0.005 0.001 HIS C 322 PHE 0.010 0.001 PHE C 196 TYR 0.010 0.001 TYR R 395 ARG 0.004 0.000 ARG D 314 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 347) hydrogen bonds : angle 4.46461 ( 1008) SS BOND : bond 0.00340 ( 4) SS BOND : angle 1.03680 ( 8) covalent geometry : bond 0.00253 ( 6754) covalent geometry : angle 0.47869 ( 9252) ********************** 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: 18 poor density : 139 time to evaluate : 1.088 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 33 GLU cc_start: 0.7307 (tt0) cc_final: 0.7093 (tt0) REVERT: C 333 GLN cc_start: 0.8436 (tp40) cc_final: 0.8116 (tp40) REVERT: D 105 TYR cc_start: 0.7856 (t80) cc_final: 0.7073 (t80) outliers start: 18 outliers final: 14 residues processed: 152 average time/residue: 0.2848 time to fit residues: 62.0128 Evaluate side-chains 153 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 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 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 7 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.169941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.132342 restraints weight = 25410.605| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.03 r_work: 0.3793 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6758 Z= 0.122 Angle : 0.482 4.254 9260 Z= 0.260 Chirality : 0.037 0.142 1141 Planarity : 0.003 0.037 1155 Dihedral : 3.868 49.254 1074 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.65 % Allowed : 21.68 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.29), residues: 892 helix: 2.56 (0.27), residues: 375 sheet: -1.29 (0.40), residues: 149 loop : -1.00 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 63 HIS 0.005 0.001 HIS C 322 PHE 0.011 0.001 PHE R 342 TYR 0.010 0.001 TYR R 395 ARG 0.003 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 347) hydrogen bonds : angle 4.45928 ( 1008) SS BOND : bond 0.00233 ( 4) SS BOND : angle 1.15309 ( 8) covalent geometry : bond 0.00263 ( 6754) covalent geometry : angle 0.48116 ( 9252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8696.45 seconds wall clock time: 152 minutes 46.80 seconds (9166.80 seconds total)