Starting phenix.real_space_refine on Sat May 2 18:43:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uxy_42789/05_2026/8uxy_42789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uxy_42789/05_2026/8uxy_42789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uxy_42789/05_2026/8uxy_42789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uxy_42789/05_2026/8uxy_42789.map" model { file = "/net/cci-nas-00/data/ceres_data/8uxy_42789/05_2026/8uxy_42789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uxy_42789/05_2026/8uxy_42789.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5174 2.51 5 N 1408 2.21 5 O 1512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8150 Number of models: 1 Model: "" Number of chains: 6 Chain: "Z" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "Y" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "X" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1840 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "A" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2309 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 12, 'TRANS': 281} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'XUQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.83, per 1000 atoms: 0.22 Number of scatterers: 8150 At special positions: 0 Unit cell: (83.42, 102.34, 140.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1512 8.00 N 1408 7.00 C 5174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 189 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 385.7 milliseconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 44.1% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'Z' and resid 7 through 24 removed outlier: 4.200A pdb=" N GLN Z 11 " --> pdb=" O ALA Z 7 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 44 removed outlier: 3.797A pdb=" N CYS Z 41 " --> pdb=" O LEU Z 37 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU Z 42 " --> pdb=" O MET Z 38 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 48 Processing helix chain 'Y' and resid 4 through 26 Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Y' and resid 35 through 37 No H-bonds generated for 'chain 'Y' and resid 35 through 37' Processing helix chain 'X' and resid 15 through 40 removed outlier: 3.866A pdb=" N LYS X 25 " --> pdb=" O GLU X 21 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE X 26 " --> pdb=" O ALA X 22 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS X 28 " --> pdb=" O LYS X 24 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG X 38 " --> pdb=" O LYS X 34 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA X 39 " --> pdb=" O GLN X 35 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR X 40 " --> pdb=" O VAL X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 60 removed outlier: 3.789A pdb=" N MET X 60 " --> pdb=" O ILE X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 233 through 239 removed outlier: 3.741A pdb=" N ASN X 239 " --> pdb=" O GLN X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 279 removed outlier: 3.719A pdb=" N ALA X 269 " --> pdb=" O ARG X 265 " (cutoff:3.500A) Processing helix chain 'X' and resid 280 through 283 removed outlier: 3.955A pdb=" N ARG X 283 " --> pdb=" O ARG X 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 280 through 283' Processing helix chain 'X' and resid 293 through 304 removed outlier: 3.683A pdb=" N GLY X 304 " --> pdb=" O LYS X 300 " (cutoff:3.500A) Processing helix chain 'X' and resid 307 through 318 Proline residue: X 313 - end of helix removed outlier: 3.546A pdb=" N TYR X 318 " --> pdb=" O PHE X 315 " (cutoff:3.500A) Processing helix chain 'X' and resid 331 through 352 removed outlier: 3.932A pdb=" N THR X 335 " --> pdb=" O ASP X 331 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE X 345 " --> pdb=" O ILE X 341 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE X 348 " --> pdb=" O GLU X 344 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER X 352 " --> pdb=" O ILE X 348 " (cutoff:3.500A) Processing helix chain 'X' and resid 370 through 391 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.617A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.713A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.991A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.638A pdb=" N ASP A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 87 removed outlier: 3.922A pdb=" N THR A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Proline residue: A 79 - end of helix Processing helix chain 'A' and resid 94 through 128 removed outlier: 4.090A pdb=" N LEU A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'A' and resid 137 through 165 removed outlier: 3.571A pdb=" N CYS A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 Processing helix chain 'A' and resid 192 through 228 Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 232 through 260 removed outlier: 4.571A pdb=" N LYS A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 289 removed outlier: 3.888A pdb=" N THR A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Proline residue: A 282 - end of helix Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 293 through 303 Processing sheet with id=AA1, first strand: chain 'Y' and resid 46 through 51 removed outlier: 5.308A pdb=" N THR Y 47 " --> pdb=" O ASN Y 340 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN Y 340 " --> pdb=" O THR Y 47 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG Y 49 " --> pdb=" O ILE Y 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Y' and resid 58 through 63 removed outlier: 4.058A pdb=" N ALA Y 60 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA Y 73 " --> pdb=" O ALA Y 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL Y 71 " --> pdb=" O HIS Y 62 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER Y 74 " --> pdb=" O LYS Y 78 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS Y 78 " --> pdb=" O SER Y 74 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS Y 91 " --> pdb=" O ILE Y 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 102 through 105 removed outlier: 4.054A pdb=" N GLY Y 115 " --> pdb=" O THR Y 102 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA Y 113 " --> pdb=" O ALA Y 104 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS Y 121 " --> pdb=" O GLU Y 138 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU Y 138 " --> pdb=" O CYS Y 121 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE Y 123 " --> pdb=" O SER Y 136 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN Y 125 " --> pdb=" O ARG Y 134 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG Y 134 " --> pdb=" O ASN Y 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Y' and resid 146 through 151 removed outlier: 3.759A pdb=" N CYS Y 148 " --> pdb=" O SER Y 160 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE Y 157 " --> pdb=" O TRP Y 169 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR Y 178 " --> pdb=" O LEU Y 168 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP Y 170 " --> pdb=" O GLN Y 176 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN Y 176 " --> pdb=" O ASP Y 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 187 through 192 removed outlier: 7.142A pdb=" N GLY Y 202 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU Y 190 " --> pdb=" O VAL Y 200 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL Y 200 " --> pdb=" O LEU Y 190 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU Y 192 " --> pdb=" O LEU Y 198 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU Y 198 " --> pdb=" O LEU Y 192 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE Y 199 " --> pdb=" O TRP Y 211 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER Y 207 " --> pdb=" O ALA Y 203 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA Y 208 " --> pdb=" O THR Y 221 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N THR Y 221 " --> pdb=" O ALA Y 208 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU Y 210 " --> pdb=" O ARG Y 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Y' and resid 233 through 234 removed outlier: 3.509A pdb=" N PHE Y 241 " --> pdb=" O PHE Y 253 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET Y 262 " --> pdb=" O LEU Y 252 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP Y 254 " --> pdb=" O GLU Y 260 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU Y 260 " --> pdb=" O ASP Y 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 273 through 278 removed outlier: 3.943A pdb=" N SER Y 275 " --> pdb=" O GLY Y 288 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY Y 306 " --> pdb=" O VAL Y 296 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP Y 298 " --> pdb=" O ARG Y 304 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG Y 304 " --> pdb=" O ASP Y 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 208 through 214 removed outlier: 5.996A pdb=" N HIS X 41 " --> pdb=" O HIS X 220 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE X 222 " --> pdb=" O HIS X 41 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU X 43 " --> pdb=" O PHE X 222 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG X 42 " --> pdb=" O ALA X 243 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE X 245 " --> pdb=" O ARG X 42 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU X 44 " --> pdb=" O ILE X 245 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL X 247 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU X 46 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ASP X 249 " --> pdb=" O LEU X 46 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE X 244 " --> pdb=" O ILE X 288 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE X 290 " --> pdb=" O ILE X 244 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE X 246 " --> pdb=" O PHE X 290 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASN X 292 " --> pdb=" O PHE X 246 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL X 248 " --> pdb=" O ASN X 292 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL X 287 " --> pdb=" O TYR X 360 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N HIS X 362 " --> pdb=" O VAL X 287 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU X 289 " --> pdb=" O HIS X 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.578A pdb=" N SER N 7 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.537A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 91 through 93 removed outlier: 8.120A pdb=" N ILE A 174 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 13 " --> pdb=" O ILE A 174 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1317 1.30 - 1.43: 2193 1.43 - 1.56: 4724 1.56 - 1.68: 1 1.68 - 1.81: 80 Bond restraints: 8315 Sorted by residual: bond pdb=" C PRO N 102 " pdb=" O PRO N 102 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.10e-02 8.26e+03 2.44e+01 bond pdb=" C LEU A 110 " pdb=" O LEU A 110 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.17e-02 7.31e+03 2.28e+01 bond pdb=" C PHE A 113 " pdb=" O PHE A 113 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.32e-02 5.74e+03 2.24e+01 bond pdb=" C ASP A 111 " pdb=" O ASP A 111 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.26e-02 6.30e+03 1.63e+01 bond pdb=" C SER A 112 " pdb=" O SER A 112 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.19e-02 7.06e+03 1.32e+01 ... (remaining 8310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 11176 4.09 - 8.17: 58 8.17 - 12.26: 12 12.26 - 16.35: 10 16.35 - 20.43: 6 Bond angle restraints: 11262 Sorted by residual: angle pdb=" C ASP Y 291 " pdb=" N PHE Y 292 " pdb=" CA PHE Y 292 " ideal model delta sigma weight residual 123.47 143.22 -19.75 1.53e+00 4.27e-01 1.67e+02 angle pdb=" C ASP X 215 " pdb=" N LYS X 216 " pdb=" CA LYS X 216 " ideal model delta sigma weight residual 122.07 137.05 -14.98 1.43e+00 4.89e-01 1.10e+02 angle pdb=" C THR Y 181 " pdb=" N GLY Y 182 " pdb=" CA GLY Y 182 " ideal model delta sigma weight residual 121.41 141.84 -20.43 1.96e+00 2.60e-01 1.09e+02 angle pdb=" C ARG Y 52 " pdb=" N GLY Y 53 " pdb=" CA GLY Y 53 " ideal model delta sigma weight residual 121.41 141.83 -20.42 1.96e+00 2.60e-01 1.08e+02 angle pdb=" C ALA Y 140 " pdb=" N GLY Y 141 " pdb=" CA GLY Y 141 " ideal model delta sigma weight residual 121.41 141.55 -20.14 1.96e+00 2.60e-01 1.06e+02 ... (remaining 11257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4567 17.64 - 35.27: 347 35.27 - 52.91: 51 52.91 - 70.54: 6 70.54 - 88.18: 9 Dihedral angle restraints: 4980 sinusoidal: 1963 harmonic: 3017 Sorted by residual: dihedral pdb=" C LEU A 55 " pdb=" N LEU A 55 " pdb=" CA LEU A 55 " pdb=" CB LEU A 55 " ideal model delta harmonic sigma weight residual -122.60 -161.56 38.96 0 2.50e+00 1.60e-01 2.43e+02 dihedral pdb=" N LEU A 55 " pdb=" C LEU A 55 " pdb=" CA LEU A 55 " pdb=" CB LEU A 55 " ideal model delta harmonic sigma weight residual 122.80 160.40 -37.60 0 2.50e+00 1.60e-01 2.26e+02 dihedral pdb=" CB CYS A 97 " pdb=" SG CYS A 97 " pdb=" SG CYS A 179 " pdb=" CB CYS A 179 " ideal model delta sinusoidal sigma weight residual -86.00 -124.02 38.02 1 1.00e+01 1.00e-02 2.04e+01 ... (remaining 4977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 1285 0.330 - 0.659: 0 0.659 - 0.989: 0 0.989 - 1.319: 0 1.319 - 1.648: 1 Chirality restraints: 1286 Sorted by residual: chirality pdb=" CA LEU A 55 " pdb=" N LEU A 55 " pdb=" C LEU A 55 " pdb=" CB LEU A 55 " both_signs ideal model delta sigma weight residual False 2.51 0.86 1.65 2.00e-01 2.50e+01 6.79e+01 chirality pdb=" CA ILE X 308 " pdb=" N ILE X 308 " pdb=" C ILE X 308 " pdb=" CB ILE X 308 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C13 XUQ A 401 " pdb=" C23 XUQ A 401 " pdb=" C63 XUQ A 401 " pdb=" O13 XUQ A 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.55 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1283 not shown) Planarity restraints: 1428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO N 100 " 0.027 2.00e-02 2.50e+03 5.17e-02 2.67e+01 pdb=" C PRO N 100 " -0.089 2.00e-02 2.50e+03 pdb=" O PRO N 100 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA N 101 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 149 " 0.034 2.00e-02 2.50e+03 2.81e-02 1.97e+01 pdb=" CG TRP A 149 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP A 149 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 149 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 149 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 149 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 149 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 149 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 149 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 149 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 111 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ASP A 111 " 0.060 2.00e-02 2.50e+03 pdb=" O ASP A 111 " -0.022 2.00e-02 2.50e+03 pdb=" N SER A 112 " -0.021 2.00e-02 2.50e+03 ... (remaining 1425 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 9 2.29 - 2.94: 3479 2.94 - 3.59: 11131 3.59 - 4.25: 16598 4.25 - 4.90: 29505 Nonbonded interactions: 60722 Sorted by model distance: nonbonded pdb=" OE2 GLU X 392 " pdb=" OD1 ASN A 293 " model vdw 1.636 3.040 nonbonded pdb=" O VAL A 83 " pdb=" OG1 THR A 87 " model vdw 2.096 3.040 nonbonded pdb=" CD GLU X 392 " pdb=" OD1 ASN A 293 " model vdw 2.115 3.270 nonbonded pdb=" O GLN Y 75 " pdb=" OG SER Y 98 " model vdw 2.153 3.040 nonbonded pdb=" OG1 THR Y 86 " pdb=" OD1 ASN Y 88 " model vdw 2.157 3.040 ... (remaining 60717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.950 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5190 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 0.062 8317 Z= 0.240 Angle : 1.014 20.432 11266 Z= 0.633 Chirality : 0.062 1.648 1286 Planarity : 0.005 0.052 1428 Dihedral : 12.756 88.177 3022 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.06 % Favored : 97.75 % Rotamer: Outliers : 0.45 % Allowed : 0.45 % Favored : 99.11 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.26), residues: 1021 helix: 2.01 (0.26), residues: 401 sheet: 0.05 (0.37), residues: 204 loop : -0.65 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Y 314 TYR 0.029 0.001 TYR A 277 PHE 0.042 0.002 PHE A 113 TRP 0.077 0.002 TRP A 149 HIS 0.006 0.001 HIS Y 183 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8315) covalent geometry : angle 1.01433 (11262) SS BOND : bond 0.00215 ( 2) SS BOND : angle 0.65065 ( 4) hydrogen bonds : bond 0.23458 ( 395) hydrogen bonds : angle 6.63716 ( 1113) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 212 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: Y 44 GLN cc_start: 0.6765 (pm20) cc_final: 0.6495 (mt0) REVERT: Y 96 ARG cc_start: 0.6349 (ttm-80) cc_final: 0.5715 (mtp-110) REVERT: Y 262 MET cc_start: 0.6164 (ptm) cc_final: 0.5805 (ptm) REVERT: Y 267 ASP cc_start: 0.7724 (m-30) cc_final: 0.6981 (p0) REVERT: Y 268 ASN cc_start: 0.7318 (m-40) cc_final: 0.7101 (t0) REVERT: X 252 ASP cc_start: 0.5885 (t0) cc_final: 0.5302 (p0) REVERT: X 369 THR cc_start: 0.6892 (p) cc_final: 0.6689 (m) REVERT: A 154 LEU cc_start: 0.5457 (tp) cc_final: 0.4900 (mt) REVERT: A 178 PHE cc_start: 0.7075 (p90) cc_final: 0.6848 (p90) REVERT: A 263 LEU cc_start: 0.8014 (mt) cc_final: 0.7232 (pt) outliers start: 4 outliers final: 1 residues processed: 214 average time/residue: 0.1060 time to fit residues: 29.4935 Evaluate side-chains 118 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 88 ASN Y 220 GLN Y 259 GLN X 23 ASN X 218 ASN X 292 ASN A 65 ASN A 109 ASN A 159 HIS A 195 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.200782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.184036 restraints weight = 9608.996| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 0.81 r_work: 0.3707 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8317 Z= 0.160 Angle : 0.599 8.847 11266 Z= 0.326 Chirality : 0.043 0.168 1286 Planarity : 0.005 0.044 1428 Dihedral : 4.328 18.102 1143 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.57 % Allowed : 8.82 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1021 helix: 2.35 (0.25), residues: 408 sheet: 0.01 (0.35), residues: 203 loop : -0.82 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 347 TYR 0.022 0.002 TYR A 277 PHE 0.019 0.002 PHE A 251 TRP 0.045 0.002 TRP A 149 HIS 0.006 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8315) covalent geometry : angle 0.59863 (11262) SS BOND : bond 0.00053 ( 2) SS BOND : angle 0.63664 ( 4) hydrogen bonds : bond 0.05751 ( 395) hydrogen bonds : angle 4.59298 ( 1113) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.291 Fit side-chains REVERT: Z 42 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7856 (tt0) REVERT: Y 44 GLN cc_start: 0.7869 (pm20) cc_final: 0.7565 (mt0) REVERT: Y 93 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7344 (mm) REVERT: X 381 ASP cc_start: 0.7728 (t70) cc_final: 0.7123 (m-30) REVERT: A 154 LEU cc_start: 0.7208 (tp) cc_final: 0.6514 (mt) REVERT: A 177 PHE cc_start: 0.4850 (p90) cc_final: 0.4495 (p90) outliers start: 23 outliers final: 16 residues processed: 123 average time/residue: 0.0823 time to fit residues: 14.3027 Evaluate side-chains 104 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 74 SER Chi-restraints excluded: chain Y residue 93 ILE Chi-restraints excluded: chain Y residue 135 VAL Chi-restraints excluded: chain Y residue 158 VAL Chi-restraints excluded: chain Y residue 245 SER Chi-restraints excluded: chain X residue 215 ASP Chi-restraints excluded: chain X residue 248 VAL Chi-restraints excluded: chain X residue 276 ILE Chi-restraints excluded: chain X residue 319 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 75 GLN Y 259 GLN X 213 GLN A 159 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.178677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161238 restraints weight = 9398.881| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 0.88 r_work: 0.3606 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8317 Z= 0.171 Angle : 0.593 7.666 11266 Z= 0.321 Chirality : 0.043 0.161 1286 Planarity : 0.004 0.045 1428 Dihedral : 4.338 18.948 1141 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.79 % Allowed : 11.27 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.26), residues: 1021 helix: 2.39 (0.25), residues: 411 sheet: -0.13 (0.34), residues: 220 loop : -0.99 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 347 TYR 0.023 0.002 TYR A 277 PHE 0.023 0.002 PHE A 211 TRP 0.031 0.002 TRP A 149 HIS 0.007 0.002 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8315) covalent geometry : angle 0.59299 (11262) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.92654 ( 4) hydrogen bonds : bond 0.06613 ( 395) hydrogen bonds : angle 4.30142 ( 1113) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.245 Fit side-chains REVERT: Y 44 GLN cc_start: 0.7948 (pm20) cc_final: 0.7674 (mt0) REVERT: Y 93 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.8028 (mm) REVERT: Y 211 TRP cc_start: 0.8060 (OUTLIER) cc_final: 0.6505 (m-10) REVERT: Y 273 ILE cc_start: 0.8499 (mp) cc_final: 0.8272 (mp) REVERT: X 368 ASP cc_start: 0.5867 (t0) cc_final: 0.5226 (p0) REVERT: A 259 TYR cc_start: 0.7895 (m-80) cc_final: 0.7669 (m-80) outliers start: 25 outliers final: 11 residues processed: 129 average time/residue: 0.0951 time to fit residues: 16.5515 Evaluate side-chains 92 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 74 SER Chi-restraints excluded: chain Y residue 93 ILE Chi-restraints excluded: chain Y residue 135 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 158 VAL Chi-restraints excluded: chain Y residue 211 TRP Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 64 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 0.0570 chunk 52 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 59 ASN X 213 GLN A 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.177946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.150704 restraints weight = 9558.262| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.17 r_work: 0.3351 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8317 Z= 0.120 Angle : 0.511 8.000 11266 Z= 0.274 Chirality : 0.041 0.156 1286 Planarity : 0.004 0.044 1428 Dihedral : 4.100 17.166 1141 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.90 % Allowed : 12.61 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.26), residues: 1021 helix: 2.73 (0.25), residues: 405 sheet: 0.05 (0.34), residues: 225 loop : -0.91 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 251 TYR 0.021 0.001 TYR A 277 PHE 0.018 0.002 PHE A 251 TRP 0.021 0.001 TRP A 149 HIS 0.008 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8315) covalent geometry : angle 0.51099 (11262) SS BOND : bond 0.00092 ( 2) SS BOND : angle 0.34842 ( 4) hydrogen bonds : bond 0.05300 ( 395) hydrogen bonds : angle 4.02116 ( 1113) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.299 Fit side-chains REVERT: Y 44 GLN cc_start: 0.7968 (pm20) cc_final: 0.7625 (mt0) REVERT: Y 93 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8020 (mm) REVERT: Y 211 TRP cc_start: 0.7836 (OUTLIER) cc_final: 0.6217 (m-10) REVERT: Y 245 SER cc_start: 0.8553 (m) cc_final: 0.8322 (t) REVERT: Y 273 ILE cc_start: 0.8614 (mp) cc_final: 0.8392 (mp) REVERT: X 368 ASP cc_start: 0.5917 (t0) cc_final: 0.5077 (p0) outliers start: 26 outliers final: 19 residues processed: 104 average time/residue: 0.0813 time to fit residues: 11.7918 Evaluate side-chains 99 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 47 THR Chi-restraints excluded: chain Y residue 74 SER Chi-restraints excluded: chain Y residue 93 ILE Chi-restraints excluded: chain Y residue 135 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 158 VAL Chi-restraints excluded: chain Y residue 211 TRP Chi-restraints excluded: chain Y residue 243 THR Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 263 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 0.0370 chunk 91 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 132 ASN ** Y 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 340 ASN X 35 GLN A 109 ASN A 159 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.153675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114814 restraints weight = 9875.261| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.95 r_work: 0.3074 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8317 Z= 0.197 Angle : 0.606 7.672 11266 Z= 0.328 Chirality : 0.044 0.156 1286 Planarity : 0.004 0.045 1428 Dihedral : 4.456 18.636 1141 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.68 % Allowed : 13.17 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.26), residues: 1021 helix: 2.35 (0.25), residues: 411 sheet: -0.30 (0.34), residues: 228 loop : -1.14 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 105 TYR 0.022 0.002 TYR A 277 PHE 0.022 0.003 PHE A 251 TRP 0.012 0.002 TRP A 149 HIS 0.008 0.002 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 8315) covalent geometry : angle 0.60615 (11262) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.22666 ( 4) hydrogen bonds : bond 0.07107 ( 395) hydrogen bonds : angle 4.25478 ( 1113) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: Y 44 GLN cc_start: 0.8086 (pm20) cc_final: 0.7490 (mt0) REVERT: Y 137 ARG cc_start: 0.7953 (mmm-85) cc_final: 0.7744 (mmm160) REVERT: Y 211 TRP cc_start: 0.7979 (OUTLIER) cc_final: 0.5930 (m-10) REVERT: X 36 VAL cc_start: 0.7865 (t) cc_final: 0.7586 (p) REVERT: X 368 ASP cc_start: 0.6394 (t0) cc_final: 0.5261 (p0) REVERT: N 19 ARG cc_start: 0.8376 (tpt-90) cc_final: 0.8128 (ttt-90) REVERT: N 60 TYR cc_start: 0.9021 (m-80) cc_final: 0.8699 (m-80) REVERT: A 81 MET cc_start: 0.7565 (tmm) cc_final: 0.7360 (tmm) outliers start: 33 outliers final: 20 residues processed: 109 average time/residue: 0.0856 time to fit residues: 12.8446 Evaluate side-chains 95 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 47 THR Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 74 SER Chi-restraints excluded: chain Y residue 135 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 211 TRP Chi-restraints excluded: chain Y residue 243 THR Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain X residue 60 MET Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 228 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 25 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.156895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117105 restraints weight = 9792.275| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.06 r_work: 0.3153 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.6899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8317 Z= 0.125 Angle : 0.500 7.943 11266 Z= 0.270 Chirality : 0.041 0.169 1286 Planarity : 0.004 0.047 1428 Dihedral : 4.119 17.501 1141 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.57 % Allowed : 15.18 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.26), residues: 1021 helix: 2.55 (0.25), residues: 411 sheet: -0.25 (0.34), residues: 229 loop : -1.12 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 105 TYR 0.019 0.001 TYR A 277 PHE 0.018 0.002 PHE A 251 TRP 0.013 0.001 TRP A 149 HIS 0.004 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8315) covalent geometry : angle 0.50012 (11262) SS BOND : bond 0.00066 ( 2) SS BOND : angle 0.22630 ( 4) hydrogen bonds : bond 0.05470 ( 395) hydrogen bonds : angle 3.98282 ( 1113) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.226 Fit side-chains REVERT: Z 46 LYS cc_start: 0.8355 (pttm) cc_final: 0.8097 (ptpt) REVERT: Y 44 GLN cc_start: 0.8087 (pm20) cc_final: 0.7472 (mt0) REVERT: Y 137 ARG cc_start: 0.7880 (mmm-85) cc_final: 0.7622 (mmm160) REVERT: Y 211 TRP cc_start: 0.7927 (OUTLIER) cc_final: 0.6159 (m-10) REVERT: X 368 ASP cc_start: 0.6320 (t0) cc_final: 0.5195 (p0) REVERT: N 60 TYR cc_start: 0.9010 (m-80) cc_final: 0.8737 (m-80) REVERT: A 81 MET cc_start: 0.7609 (tmm) cc_final: 0.7307 (tmm) outliers start: 23 outliers final: 19 residues processed: 102 average time/residue: 0.0975 time to fit residues: 13.4090 Evaluate side-chains 91 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 47 THR Chi-restraints excluded: chain Y residue 74 SER Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 118 ASP Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 211 TRP Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Y residue 322 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 228 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 23 ASN A 109 ASN A 159 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.157444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117777 restraints weight = 9860.721| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.07 r_work: 0.3137 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.7004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8317 Z= 0.106 Angle : 0.488 7.768 11266 Z= 0.259 Chirality : 0.040 0.200 1286 Planarity : 0.003 0.047 1428 Dihedral : 3.951 16.928 1141 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.46 % Allowed : 16.07 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.26), residues: 1021 helix: 2.78 (0.25), residues: 405 sheet: -0.12 (0.34), residues: 227 loop : -1.05 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 105 TYR 0.019 0.001 TYR A 277 PHE 0.017 0.001 PHE A 251 TRP 0.013 0.001 TRP A 149 HIS 0.003 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 8315) covalent geometry : angle 0.48764 (11262) SS BOND : bond 0.00206 ( 2) SS BOND : angle 0.47739 ( 4) hydrogen bonds : bond 0.04934 ( 395) hydrogen bonds : angle 3.86232 ( 1113) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.355 Fit side-chains REVERT: Z 46 LYS cc_start: 0.8324 (pttm) cc_final: 0.8068 (ptpt) REVERT: Y 32 GLN cc_start: 0.7537 (pt0) cc_final: 0.7130 (pt0) REVERT: Y 44 GLN cc_start: 0.8069 (pm20) cc_final: 0.7453 (mt0) REVERT: Y 137 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7551 (mmm160) REVERT: Y 211 TRP cc_start: 0.7912 (OUTLIER) cc_final: 0.6217 (m-10) REVERT: X 23 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.7093 (t0) REVERT: X 368 ASP cc_start: 0.6224 (t0) cc_final: 0.5067 (p0) REVERT: N 60 TYR cc_start: 0.9026 (m-80) cc_final: 0.8785 (m-80) REVERT: A 81 MET cc_start: 0.7685 (tmm) cc_final: 0.7359 (tmm) outliers start: 22 outliers final: 19 residues processed: 90 average time/residue: 0.0980 time to fit residues: 11.8991 Evaluate side-chains 91 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 47 THR Chi-restraints excluded: chain Y residue 74 SER Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 118 ASP Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 211 TRP Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Y residue 322 ASP Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 284 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 228 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 0.0770 chunk 83 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.158667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.119401 restraints weight = 9743.203| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.02 r_work: 0.3147 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8317 Z= 0.102 Angle : 0.470 7.769 11266 Z= 0.250 Chirality : 0.040 0.157 1286 Planarity : 0.003 0.047 1428 Dihedral : 3.867 16.680 1141 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.57 % Allowed : 16.41 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.26), residues: 1021 helix: 2.87 (0.25), residues: 405 sheet: 0.03 (0.34), residues: 217 loop : -1.08 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.018 0.001 TYR A 277 PHE 0.017 0.001 PHE A 251 TRP 0.012 0.001 TRP A 149 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 8315) covalent geometry : angle 0.47007 (11262) SS BOND : bond 0.00083 ( 2) SS BOND : angle 0.43366 ( 4) hydrogen bonds : bond 0.04724 ( 395) hydrogen bonds : angle 3.78405 ( 1113) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.302 Fit side-chains REVERT: Y 32 GLN cc_start: 0.7581 (pt0) cc_final: 0.6990 (pt0) REVERT: Y 44 GLN cc_start: 0.8068 (pm20) cc_final: 0.7430 (mt0) REVERT: Y 93 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7808 (mm) REVERT: Y 137 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7608 (mmm160) REVERT: Y 211 TRP cc_start: 0.7889 (OUTLIER) cc_final: 0.6239 (m-10) REVERT: X 307 LYS cc_start: 0.8814 (mttp) cc_final: 0.8225 (mtmt) REVERT: X 368 ASP cc_start: 0.6224 (t0) cc_final: 0.5052 (p0) REVERT: N 60 TYR cc_start: 0.9015 (m-80) cc_final: 0.8777 (m-80) REVERT: A 81 MET cc_start: 0.7820 (tmm) cc_final: 0.7552 (tmm) outliers start: 23 outliers final: 19 residues processed: 94 average time/residue: 0.1039 time to fit residues: 13.1383 Evaluate side-chains 92 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 47 THR Chi-restraints excluded: chain Y residue 93 ILE Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 118 ASP Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 211 TRP Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Y residue 322 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 284 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 228 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 18 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 chunk 77 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.157216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117372 restraints weight = 9824.565| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.06 r_work: 0.3151 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.7139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8317 Z= 0.106 Angle : 0.480 9.829 11266 Z= 0.253 Chirality : 0.040 0.255 1286 Planarity : 0.003 0.047 1428 Dihedral : 3.830 16.751 1141 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.79 % Allowed : 16.18 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.26), residues: 1021 helix: 2.92 (0.25), residues: 405 sheet: 0.07 (0.34), residues: 217 loop : -1.06 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.018 0.001 TYR A 277 PHE 0.017 0.001 PHE A 251 TRP 0.011 0.001 TRP A 149 HIS 0.004 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 8315) covalent geometry : angle 0.47967 (11262) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.40015 ( 4) hydrogen bonds : bond 0.04723 ( 395) hydrogen bonds : angle 3.76670 ( 1113) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.230 Fit side-chains REVERT: Y 32 GLN cc_start: 0.7567 (pt0) cc_final: 0.7239 (pt0) REVERT: Y 44 GLN cc_start: 0.8070 (pm20) cc_final: 0.7442 (mt0) REVERT: Y 137 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7624 (mmm160) REVERT: Y 211 TRP cc_start: 0.7908 (OUTLIER) cc_final: 0.6264 (m-10) REVERT: X 307 LYS cc_start: 0.8837 (mttp) cc_final: 0.8262 (mtmt) REVERT: X 368 ASP cc_start: 0.6268 (t0) cc_final: 0.5089 (p0) REVERT: N 60 TYR cc_start: 0.9003 (m-80) cc_final: 0.8764 (m-80) REVERT: A 81 MET cc_start: 0.7807 (tmm) cc_final: 0.7536 (tmm) outliers start: 25 outliers final: 20 residues processed: 94 average time/residue: 0.1032 time to fit residues: 13.0412 Evaluate side-chains 93 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 47 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 118 ASP Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 211 TRP Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Y residue 322 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 248 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 228 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 0.0770 chunk 60 optimal weight: 0.0970 chunk 25 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.157858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118542 restraints weight = 9708.482| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.91 r_work: 0.3144 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.7221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8317 Z= 0.115 Angle : 0.489 8.875 11266 Z= 0.258 Chirality : 0.040 0.230 1286 Planarity : 0.003 0.047 1428 Dihedral : 3.860 16.889 1141 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.46 % Allowed : 16.52 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.26), residues: 1021 helix: 2.92 (0.25), residues: 405 sheet: 0.13 (0.35), residues: 216 loop : -1.08 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 105 TYR 0.018 0.001 TYR A 277 PHE 0.017 0.001 PHE A 251 TRP 0.010 0.001 TRP X 234 HIS 0.006 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8315) covalent geometry : angle 0.48942 (11262) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.37987 ( 4) hydrogen bonds : bond 0.04903 ( 395) hydrogen bonds : angle 3.78362 ( 1113) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.313 Fit side-chains REVERT: Y 44 GLN cc_start: 0.8079 (pm20) cc_final: 0.7468 (mt0) REVERT: Y 137 ARG cc_start: 0.7851 (mmm-85) cc_final: 0.7618 (mmm160) REVERT: Y 172 GLU cc_start: 0.7035 (tp30) cc_final: 0.6444 (tt0) REVERT: Y 211 TRP cc_start: 0.7931 (OUTLIER) cc_final: 0.6228 (m-10) REVERT: X 307 LYS cc_start: 0.8867 (mttp) cc_final: 0.8317 (mtmt) REVERT: X 368 ASP cc_start: 0.6297 (OUTLIER) cc_final: 0.5125 (p0) REVERT: N 60 TYR cc_start: 0.9012 (m-80) cc_final: 0.8776 (m-80) REVERT: A 81 MET cc_start: 0.7882 (tmm) cc_final: 0.7533 (tmm) REVERT: A 90 LYS cc_start: 0.7568 (mtmm) cc_final: 0.6928 (mttt) REVERT: A 200 PHE cc_start: 0.4413 (OUTLIER) cc_final: 0.3777 (t80) outliers start: 22 outliers final: 18 residues processed: 94 average time/residue: 0.1007 time to fit residues: 12.7654 Evaluate side-chains 94 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 47 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 118 ASP Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 211 TRP Chi-restraints excluded: chain Y residue 263 THR Chi-restraints excluded: chain Y residue 322 ASP Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 248 VAL Chi-restraints excluded: chain X residue 368 ASP Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 228 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 23 optimal weight: 0.0970 chunk 13 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 94 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 23 ASN A 109 ASN A 159 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.159913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120158 restraints weight = 9743.153| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.97 r_work: 0.3166 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.7263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8317 Z= 0.096 Angle : 0.469 8.459 11266 Z= 0.246 Chirality : 0.040 0.216 1286 Planarity : 0.003 0.048 1428 Dihedral : 3.737 16.294 1141 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.46 % Allowed : 16.74 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.26), residues: 1021 helix: 3.00 (0.25), residues: 406 sheet: 0.13 (0.34), residues: 224 loop : -1.03 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 105 TYR 0.019 0.001 TYR A 277 PHE 0.016 0.001 PHE A 251 TRP 0.012 0.001 TRP A 149 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 8315) covalent geometry : angle 0.46864 (11262) SS BOND : bond 0.00086 ( 2) SS BOND : angle 0.36673 ( 4) hydrogen bonds : bond 0.04351 ( 395) hydrogen bonds : angle 3.70255 ( 1113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2122.37 seconds wall clock time: 37 minutes 1.41 seconds (2221.41 seconds total)