Starting phenix.real_space_refine on Mon Apr 28 10:50:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f1s_31424/04_2025/7f1s_31424.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f1s_31424/04_2025/7f1s_31424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f1s_31424/04_2025/7f1s_31424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f1s_31424/04_2025/7f1s_31424.map" model { file = "/net/cci-nas-00/data/ceres_data/7f1s_31424/04_2025/7f1s_31424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f1s_31424/04_2025/7f1s_31424.cif" } resolution = 2.8 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= 0.044 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 1442 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4009 2.51 5 N 1055 2.21 5 O 1103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6209 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2051 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 127 Chain: "A" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1588 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2338 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 314} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 232 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 30} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 3.88, per 1000 atoms: 0.62 Number of scatterers: 6209 At special positions: 0 Unit cell: (113.905, 112.86, 72.105, 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 42 16.00 O 1103 8.00 N 1055 7.00 C 4009 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 101 " - pdb=" SG CYS R 178 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 853.0 milliseconds 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 45.3% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'R' and resid 33 through 58 removed outlier: 3.790A pdb=" N TYR R 37 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER R 38 " --> pdb=" O PRO R 34 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE R 41 " --> pdb=" O TYR R 37 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE R 45 " --> pdb=" O PHE R 41 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL R 46 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN R 57 " --> pdb=" O LEU R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 81 removed outlier: 4.062A pdb=" N TYR R 68 " --> pdb=" O MET R 64 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU R 69 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN R 71 " --> pdb=" O ILE R 67 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU R 72 " --> pdb=" O TYR R 68 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU R 77 " --> pdb=" O ALA R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 87 removed outlier: 4.105A pdb=" N PHE R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 132 removed outlier: 3.597A pdb=" N GLN R 102 " --> pdb=" O ASN R 98 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY R 115 " --> pdb=" O GLY R 111 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE R 120 " --> pdb=" O ILE R 116 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL R 130 " --> pdb=" O ARG R 126 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS R 132 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 140 removed outlier: 4.061A pdb=" N LYS R 138 " --> pdb=" O VAL R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 166 removed outlier: 4.079A pdb=" N VAL R 147 " --> pdb=" O THR R 143 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE R 151 " --> pdb=" O VAL R 147 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR R 152 " --> pdb=" O THR R 148 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA R 156 " --> pdb=" O THR R 152 " (cutoff:3.500A) Proline residue: R 162 - end of helix Processing helix chain 'R' and resid 186 through 201 removed outlier: 3.596A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 220 removed outlier: 3.517A pdb=" N TYR R 214 " --> pdb=" O MET R 210 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 248 removed outlier: 4.074A pdb=" N ARG R 232 " --> pdb=" O LYS R 228 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET R 241 " --> pdb=" O ILE R 237 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR R 244 " --> pdb=" O ILE R 240 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE R 245 " --> pdb=" O MET R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 260 removed outlier: 3.947A pdb=" N LEU R 257 " --> pdb=" O ILE R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 269 Processing helix chain 'R' and resid 270 through 277 removed outlier: 4.241A pdb=" N ARG R 274 " --> pdb=" O SER R 270 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN R 277 " --> pdb=" O ASN R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 288 Processing helix chain 'R' and resid 292 through 298 Processing helix chain 'R' and resid 303 through 313 removed outlier: 3.744A pdb=" N TYR R 307 " --> pdb=" O LYS R 303 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL R 310 " --> pdb=" O ASN R 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 33 removed outlier: 3.550A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.568A pdb=" N SER A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.968A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.781A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.658A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.523A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.576A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 171 removed outlier: 3.717A pdb=" N GLN R 170 " --> pdb=" O THR R 177 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N THR R 177 " --> pdb=" O GLN R 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.841A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.982A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.577A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.987A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.609A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.885A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.231A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.541A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 828 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: 1.74 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1989 1.35 - 1.46: 1606 1.46 - 1.58: 2690 1.58 - 1.70: 0 1.70 - 1.82: 57 Bond restraints: 6342 Sorted by residual: bond pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.27e+00 bond pdb=" CA LEU R 33 " pdb=" C LEU R 33 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.10e-02 2.27e+03 5.99e-01 bond pdb=" C PRO R 34 " pdb=" N PRO R 35 " ideal model delta sigma weight residual 1.336 1.345 -0.009 1.25e-02 6.40e+03 5.21e-01 bond pdb=" CB GLN R 194 " pdb=" CG GLN R 194 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 bond pdb=" CA GLU C 47 " pdb=" C GLU C 47 " ideal model delta sigma weight residual 1.526 1.535 -0.010 1.36e-02 5.41e+03 4.97e-01 ... (remaining 6337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 8501 1.62 - 3.24: 116 3.24 - 4.87: 23 4.87 - 6.49: 12 6.49 - 8.11: 2 Bond angle restraints: 8654 Sorted by residual: angle pdb=" C ASN R 268 " pdb=" N CYS R 269 " pdb=" CA CYS R 269 " ideal model delta sigma weight residual 121.54 126.09 -4.55 1.91e+00 2.74e-01 5.67e+00 angle pdb=" CA LEU R 161 " pdb=" CB LEU R 161 " pdb=" CG LEU R 161 " ideal model delta sigma weight residual 116.30 124.41 -8.11 3.50e+00 8.16e-02 5.37e+00 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 123.91 127.56 -3.65 1.66e+00 3.63e-01 4.82e+00 angle pdb=" N LEU B 300 " pdb=" CA LEU B 300 " pdb=" C LEU B 300 " ideal model delta sigma weight residual 114.31 111.60 2.71 1.29e+00 6.01e-01 4.40e+00 angle pdb=" C CYS R 224 " pdb=" N ARG R 225 " pdb=" CA ARG R 225 " ideal model delta sigma weight residual 122.08 125.08 -3.00 1.47e+00 4.63e-01 4.17e+00 ... (remaining 8649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3465 17.53 - 35.07: 180 35.07 - 52.60: 14 52.60 - 70.14: 6 70.14 - 87.67: 4 Dihedral angle restraints: 3669 sinusoidal: 1207 harmonic: 2462 Sorted by residual: dihedral pdb=" CA ASN R 293 " pdb=" CB ASN R 293 " pdb=" CG ASN R 293 " pdb=" OD1 ASN R 293 " ideal model delta sinusoidal sigma weight residual -90.00 -156.28 66.28 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CB LYS A 29 " pdb=" CG LYS A 29 " pdb=" CD LYS A 29 " pdb=" CE LYS A 29 " ideal model delta sinusoidal sigma weight residual 60.00 118.28 -58.28 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLN B 220 " pdb=" CB GLN B 220 " pdb=" CG GLN B 220 " pdb=" CD GLN B 220 " ideal model delta sinusoidal sigma weight residual -60.00 -105.58 45.58 3 1.50e+01 4.44e-03 8.19e+00 ... (remaining 3666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 624 0.030 - 0.061: 309 0.061 - 0.091: 66 0.091 - 0.121: 38 0.121 - 0.152: 5 Chirality restraints: 1042 Sorted by residual: chirality pdb=" CA THR B 196 " pdb=" N THR B 196 " pdb=" C THR B 196 " pdb=" CB THR B 196 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA THR B 164 " pdb=" N THR B 164 " pdb=" C THR B 164 " pdb=" CB THR B 164 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 1039 not shown) Planarity restraints: 1085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO B 39 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 33 " -0.037 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO R 34 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 34 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 34 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO B 236 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 ... (remaining 1082 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1047 2.76 - 3.30: 6289 3.30 - 3.83: 10363 3.83 - 4.37: 12405 4.37 - 4.90: 21056 Nonbonded interactions: 51160 Sorted by model distance: nonbonded pdb=" O ASN R 163 " pdb=" OG1 THR R 167 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR R 108 " pdb=" OE1 GLU R 283 " model vdw 2.252 3.040 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.259 3.120 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.296 3.120 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.332 3.120 ... (remaining 51155 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: 0.010 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.030 Find NCS groups from input model: 0.070 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:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.002 0.021 6343 Z= 0.100 Angle : 0.552 8.112 8656 Z= 0.290 Chirality : 0.039 0.152 1042 Planarity : 0.004 0.073 1085 Dihedral : 10.910 87.669 2068 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -1.65 (0.27), residues: 833 helix: -2.04 (0.24), residues: 291 sheet: 0.68 (0.41), residues: 155 loop : -0.95 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 153 HIS 0.005 0.001 HIS R 132 PHE 0.007 0.001 PHE B 151 TYR 0.015 0.001 TYR R 251 ARG 0.007 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.28763 ( 293) hydrogen bonds : angle 9.22531 ( 828) SS BOND : bond 0.00332 ( 1) SS BOND : angle 1.23197 ( 2) covalent geometry : bond 0.00192 ( 6342) covalent geometry : angle 0.55169 ( 8654) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: R 74 ILE cc_start: 0.8504 (mt) cc_final: 0.8128 (mp) REVERT: R 100 MET cc_start: 0.6810 (tmm) cc_final: 0.6562 (tmm) REVERT: R 138 LYS cc_start: 0.8182 (ptmm) cc_final: 0.7967 (pttp) REVERT: R 295 ILE cc_start: 0.8450 (tp) cc_final: 0.8133 (pp) REVERT: A 230 TYR cc_start: 0.7133 (p90) cc_final: 0.6704 (p90) REVERT: B 188 MET cc_start: 0.8085 (mmm) cc_final: 0.7831 (mmp) REVERT: B 209 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7591 (mmtm) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 1.0558 time to fit residues: 169.2145 Evaluate side-chains 101 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 GLN A 294 ASN B 176 GLN B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.115505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092202 restraints weight = 13439.787| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.05 r_work: 0.3397 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6343 Z= 0.163 Angle : 0.636 8.706 8656 Z= 0.326 Chirality : 0.043 0.145 1042 Planarity : 0.005 0.052 1085 Dihedral : 3.834 17.186 894 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.35 % Allowed : 15.44 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.28), residues: 833 helix: -0.52 (0.27), residues: 332 sheet: 0.61 (0.41), residues: 165 loop : -0.77 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 211 HIS 0.006 0.001 HIS R 132 PHE 0.015 0.002 PHE R 45 TYR 0.021 0.002 TYR R 307 ARG 0.008 0.001 ARG R 140 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 293) hydrogen bonds : angle 5.36087 ( 828) SS BOND : bond 0.00271 ( 1) SS BOND : angle 2.10635 ( 2) covalent geometry : bond 0.00353 ( 6342) covalent geometry : angle 0.63554 ( 8654) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.705 Fit side-chains REVERT: R 110 ILE cc_start: 0.8849 (mp) cc_final: 0.8504 (mp) REVERT: R 197 LYS cc_start: 0.7950 (pttp) cc_final: 0.6646 (mmpt) REVERT: R 225 ARG cc_start: 0.7750 (ptm-80) cc_final: 0.7516 (ptm-80) REVERT: R 235 ARG cc_start: 0.7336 (tpt170) cc_final: 0.6992 (tpt170) REVERT: R 280 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7990 (tp-100) REVERT: R 297 TYR cc_start: 0.9208 (m-80) cc_final: 0.8959 (m-80) REVERT: A 21 ARG cc_start: 0.8352 (ttp-110) cc_final: 0.8147 (ttp-110) REVERT: A 186 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7603 (mt-10) REVERT: A 230 TYR cc_start: 0.7819 (p90) cc_final: 0.7338 (p90) REVERT: A 304 GLN cc_start: 0.8815 (tt0) cc_final: 0.8542 (tt0) REVERT: B 188 MET cc_start: 0.9030 (mmm) cc_final: 0.8690 (mmm) REVERT: B 228 ASP cc_start: 0.8007 (p0) cc_final: 0.7690 (p0) REVERT: B 230 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.7979 (m110) outliers start: 14 outliers final: 6 residues processed: 130 average time/residue: 1.0941 time to fit residues: 149.6670 Evaluate side-chains 112 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.113682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.090434 restraints weight = 13547.805| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.03 r_work: 0.3362 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6343 Z= 0.148 Angle : 0.600 8.718 8656 Z= 0.308 Chirality : 0.042 0.165 1042 Planarity : 0.004 0.052 1085 Dihedral : 3.733 17.678 894 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.85 % Allowed : 17.62 % Favored : 79.53 % 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: -0.27 (0.29), residues: 833 helix: 0.08 (0.28), residues: 332 sheet: 0.64 (0.40), residues: 168 loop : -0.75 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS R 132 PHE 0.011 0.001 PHE B 222 TYR 0.015 0.001 TYR R 307 ARG 0.007 0.001 ARG R 140 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 293) hydrogen bonds : angle 4.86316 ( 828) SS BOND : bond 0.00219 ( 1) SS BOND : angle 1.53301 ( 2) covalent geometry : bond 0.00331 ( 6342) covalent geometry : angle 0.60005 ( 8654) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: R 110 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8577 (mp) REVERT: R 235 ARG cc_start: 0.7354 (tpt170) cc_final: 0.6863 (tpt170) REVERT: R 241 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.8034 (mmt) REVERT: R 280 GLN cc_start: 0.8284 (tp-100) cc_final: 0.7995 (tp-100) REVERT: R 305 ARG cc_start: 0.7658 (mpp80) cc_final: 0.7395 (mmt90) REVERT: A 21 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.8181 (ttp-110) REVERT: A 186 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7629 (mt-10) REVERT: A 230 TYR cc_start: 0.7783 (p90) cc_final: 0.7389 (p90) REVERT: B 228 ASP cc_start: 0.8122 (p0) cc_final: 0.7794 (p0) REVERT: B 230 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.7978 (m110) outliers start: 17 outliers final: 10 residues processed: 125 average time/residue: 1.0054 time to fit residues: 132.8741 Evaluate side-chains 112 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.104626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.080661 restraints weight = 13856.277| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.87 r_work: 0.3179 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 6343 Z= 0.312 Angle : 0.717 9.572 8656 Z= 0.375 Chirality : 0.047 0.167 1042 Planarity : 0.005 0.053 1085 Dihedral : 4.309 20.707 894 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.03 % Allowed : 20.13 % Favored : 75.84 % 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: -0.37 (0.29), residues: 833 helix: 0.17 (0.27), residues: 335 sheet: -0.00 (0.39), residues: 177 loop : -0.65 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 211 HIS 0.005 0.001 HIS A 244 PHE 0.023 0.002 PHE B 292 TYR 0.016 0.002 TYR R 251 ARG 0.007 0.001 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 293) hydrogen bonds : angle 4.96553 ( 828) SS BOND : bond 0.00299 ( 1) SS BOND : angle 1.84073 ( 2) covalent geometry : bond 0.00710 ( 6342) covalent geometry : angle 0.71643 ( 8654) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.676 Fit side-chains REVERT: R 158 PHE cc_start: 0.8222 (t80) cc_final: 0.7958 (t80) REVERT: R 235 ARG cc_start: 0.7445 (tpt170) cc_final: 0.6982 (tpt170) REVERT: R 241 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8159 (mmt) REVERT: R 295 ILE cc_start: 0.8778 (tp) cc_final: 0.8358 (pp) REVERT: R 305 ARG cc_start: 0.7994 (mpp80) cc_final: 0.7780 (mmt90) REVERT: A 18 MET cc_start: 0.8322 (mmt) cc_final: 0.8114 (mmt) REVERT: A 21 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.8213 (ttp-110) REVERT: A 186 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7969 (mt-10) REVERT: A 230 TYR cc_start: 0.8127 (p90) cc_final: 0.7806 (p90) REVERT: A 251 ASP cc_start: 0.8941 (t0) cc_final: 0.8687 (t0) REVERT: B 46 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7009 (mtm-85) REVERT: B 188 MET cc_start: 0.8999 (mmm) cc_final: 0.8684 (mmm) REVERT: B 292 PHE cc_start: 0.8774 (m-80) cc_final: 0.8418 (m-80) REVERT: B 335 PHE cc_start: 0.8637 (m-10) cc_final: 0.8358 (m-80) outliers start: 24 outliers final: 14 residues processed: 119 average time/residue: 1.0816 time to fit residues: 135.6013 Evaluate side-chains 107 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.107890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.084169 restraints weight = 13590.430| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.89 r_work: 0.3242 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6343 Z= 0.150 Angle : 0.616 9.193 8656 Z= 0.319 Chirality : 0.043 0.153 1042 Planarity : 0.004 0.053 1085 Dihedral : 4.073 20.447 894 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.52 % Allowed : 21.64 % Favored : 74.83 % 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: -0.32 (0.29), residues: 833 helix: 0.32 (0.28), residues: 331 sheet: -0.12 (0.39), residues: 174 loop : -0.65 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.010 0.001 PHE B 292 TYR 0.019 0.002 TYR R 297 ARG 0.005 0.001 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 293) hydrogen bonds : angle 4.77254 ( 828) SS BOND : bond 0.00178 ( 1) SS BOND : angle 1.30160 ( 2) covalent geometry : bond 0.00341 ( 6342) covalent geometry : angle 0.61567 ( 8654) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.675 Fit side-chains REVERT: R 100 MET cc_start: 0.6483 (tmm) cc_final: 0.6000 (tmm) REVERT: R 158 PHE cc_start: 0.8173 (t80) cc_final: 0.7931 (t80) REVERT: R 235 ARG cc_start: 0.7480 (tpt170) cc_final: 0.7251 (tpt170) REVERT: R 241 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8147 (mmt) REVERT: R 295 ILE cc_start: 0.8737 (tp) cc_final: 0.8296 (pp) REVERT: R 305 ARG cc_start: 0.7943 (mpp80) cc_final: 0.7740 (mmt90) REVERT: A 18 MET cc_start: 0.8342 (mmt) cc_final: 0.8100 (mmt) REVERT: A 21 ARG cc_start: 0.8423 (ttp-110) cc_final: 0.8201 (ttp-110) REVERT: A 186 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7951 (mt-10) REVERT: A 230 TYR cc_start: 0.7918 (p90) cc_final: 0.7708 (p90) REVERT: B 188 MET cc_start: 0.8838 (mmm) cc_final: 0.8500 (mmm) REVERT: B 292 PHE cc_start: 0.8553 (m-80) cc_final: 0.8292 (m-80) REVERT: B 335 PHE cc_start: 0.8606 (m-10) cc_final: 0.8243 (m-80) outliers start: 21 outliers final: 15 residues processed: 115 average time/residue: 1.0392 time to fit residues: 126.1572 Evaluate side-chains 107 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.0030 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN A 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.108764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.085251 restraints weight = 13537.267| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.89 r_work: 0.3264 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6343 Z= 0.137 Angle : 0.593 9.084 8656 Z= 0.308 Chirality : 0.042 0.149 1042 Planarity : 0.004 0.054 1085 Dihedral : 3.941 19.532 894 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.36 % Allowed : 23.66 % Favored : 72.99 % 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: -0.17 (0.29), residues: 833 helix: 0.49 (0.28), residues: 333 sheet: -0.10 (0.39), residues: 174 loop : -0.60 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 132 PHE 0.009 0.001 PHE B 292 TYR 0.019 0.002 TYR R 297 ARG 0.008 0.001 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 293) hydrogen bonds : angle 4.60939 ( 828) SS BOND : bond 0.00239 ( 1) SS BOND : angle 1.16714 ( 2) covalent geometry : bond 0.00311 ( 6342) covalent geometry : angle 0.59319 ( 8654) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.637 Fit side-chains REVERT: R 158 PHE cc_start: 0.8172 (t80) cc_final: 0.7859 (t80) REVERT: R 235 ARG cc_start: 0.7487 (tpt170) cc_final: 0.7214 (tpt170) REVERT: R 241 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8150 (mmt) REVERT: R 295 ILE cc_start: 0.8805 (tp) cc_final: 0.8363 (pp) REVERT: R 305 ARG cc_start: 0.7955 (mpp80) cc_final: 0.7742 (mmt90) REVERT: A 18 MET cc_start: 0.8321 (mmt) cc_final: 0.8075 (mmt) REVERT: B 188 MET cc_start: 0.8822 (mmm) cc_final: 0.8538 (mmm) REVERT: B 292 PHE cc_start: 0.8431 (m-80) cc_final: 0.8207 (m-80) REVERT: B 335 PHE cc_start: 0.8591 (m-10) cc_final: 0.8230 (m-80) outliers start: 20 outliers final: 13 residues processed: 119 average time/residue: 0.9470 time to fit residues: 119.6111 Evaluate side-chains 107 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 41 optimal weight: 0.0040 chunk 14 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 ASN A 256 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.108705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.085344 restraints weight = 13620.933| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.88 r_work: 0.3267 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6343 Z= 0.140 Angle : 0.610 9.402 8656 Z= 0.315 Chirality : 0.042 0.148 1042 Planarity : 0.004 0.054 1085 Dihedral : 3.910 19.149 894 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.52 % Allowed : 24.16 % Favored : 72.32 % 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: -0.13 (0.29), residues: 833 helix: 0.55 (0.28), residues: 331 sheet: -0.13 (0.39), residues: 174 loop : -0.57 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 132 PHE 0.009 0.001 PHE B 292 TYR 0.020 0.001 TYR R 297 ARG 0.008 0.001 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 293) hydrogen bonds : angle 4.55929 ( 828) SS BOND : bond 0.00200 ( 1) SS BOND : angle 1.08781 ( 2) covalent geometry : bond 0.00317 ( 6342) covalent geometry : angle 0.60939 ( 8654) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: R 68 TYR cc_start: 0.8520 (m-80) cc_final: 0.8290 (m-10) REVERT: R 100 MET cc_start: 0.6469 (tmm) cc_final: 0.5968 (tmm) REVERT: R 158 PHE cc_start: 0.8139 (t80) cc_final: 0.7838 (t80) REVERT: R 235 ARG cc_start: 0.7474 (tpt170) cc_final: 0.7161 (tpt170) REVERT: R 241 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8152 (mmt) REVERT: R 295 ILE cc_start: 0.8845 (tp) cc_final: 0.8432 (pp) REVERT: R 305 ARG cc_start: 0.7982 (mpp80) cc_final: 0.7756 (mmt90) REVERT: A 18 MET cc_start: 0.8304 (mmt) cc_final: 0.8078 (mmt) REVERT: A 21 ARG cc_start: 0.8523 (ttp-110) cc_final: 0.8283 (ttp-110) REVERT: B 188 MET cc_start: 0.8812 (mmm) cc_final: 0.8512 (mmm) REVERT: B 234 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.8905 (m-80) REVERT: B 262 MET cc_start: 0.7605 (tpp) cc_final: 0.7338 (tpp) REVERT: B 292 PHE cc_start: 0.8424 (m-80) cc_final: 0.8148 (m-80) REVERT: B 335 PHE cc_start: 0.8583 (m-10) cc_final: 0.8196 (m-80) outliers start: 21 outliers final: 15 residues processed: 116 average time/residue: 0.9808 time to fit residues: 120.2311 Evaluate side-chains 110 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 34 optimal weight: 0.1980 chunk 73 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN B 142 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.109205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.085943 restraints weight = 13508.506| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.88 r_work: 0.3277 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6343 Z= 0.134 Angle : 0.614 9.225 8656 Z= 0.317 Chirality : 0.042 0.149 1042 Planarity : 0.004 0.054 1085 Dihedral : 3.889 18.975 894 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.36 % Allowed : 24.83 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.12 (0.29), residues: 833 helix: 0.55 (0.28), residues: 331 sheet: -0.16 (0.39), residues: 174 loop : -0.52 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 132 PHE 0.008 0.001 PHE A 196 TYR 0.017 0.002 TYR R 297 ARG 0.009 0.001 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03070 ( 293) hydrogen bonds : angle 4.56582 ( 828) SS BOND : bond 0.00244 ( 1) SS BOND : angle 1.01244 ( 2) covalent geometry : bond 0.00306 ( 6342) covalent geometry : angle 0.61396 ( 8654) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: R 68 TYR cc_start: 0.8523 (m-10) cc_final: 0.8253 (m-10) REVERT: R 100 MET cc_start: 0.6456 (tmm) cc_final: 0.5953 (tmm) REVERT: R 158 PHE cc_start: 0.8134 (t80) cc_final: 0.7869 (t80) REVERT: R 235 ARG cc_start: 0.7430 (tpt170) cc_final: 0.7155 (tpt170) REVERT: R 241 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8149 (mmt) REVERT: R 295 ILE cc_start: 0.8818 (tp) cc_final: 0.8409 (pp) REVERT: R 305 ARG cc_start: 0.7999 (mpp80) cc_final: 0.7758 (mmt90) REVERT: B 188 MET cc_start: 0.8801 (mmm) cc_final: 0.8504 (mmm) REVERT: B 234 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8904 (m-80) REVERT: B 292 PHE cc_start: 0.8394 (m-80) cc_final: 0.8167 (m-80) REVERT: B 335 PHE cc_start: 0.8573 (m-10) cc_final: 0.8192 (m-80) outliers start: 20 outliers final: 13 residues processed: 114 average time/residue: 1.0622 time to fit residues: 128.1565 Evaluate side-chains 110 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 0.1980 chunk 76 optimal weight: 0.6980 chunk 50 optimal weight: 0.0040 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.110662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.087426 restraints weight = 13642.994| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.91 r_work: 0.3303 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6343 Z= 0.121 Angle : 0.624 9.377 8656 Z= 0.319 Chirality : 0.041 0.146 1042 Planarity : 0.004 0.054 1085 Dihedral : 3.843 18.358 894 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.68 % Allowed : 26.17 % Favored : 71.14 % 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: -0.04 (0.29), residues: 833 helix: 0.60 (0.28), residues: 331 sheet: -0.22 (0.39), residues: 176 loop : -0.39 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 132 PHE 0.008 0.001 PHE A 196 TYR 0.017 0.001 TYR R 307 ARG 0.008 0.001 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.02932 ( 293) hydrogen bonds : angle 4.49511 ( 828) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.84000 ( 2) covalent geometry : bond 0.00271 ( 6342) covalent geometry : angle 0.62359 ( 8654) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: R 68 TYR cc_start: 0.8522 (m-10) cc_final: 0.8288 (m-10) REVERT: R 158 PHE cc_start: 0.8173 (t80) cc_final: 0.7860 (t80) REVERT: R 295 ILE cc_start: 0.8789 (tp) cc_final: 0.8411 (pp) REVERT: R 305 ARG cc_start: 0.7980 (mpp80) cc_final: 0.7742 (mmt90) REVERT: B 57 LYS cc_start: 0.9143 (ptpp) cc_final: 0.8514 (ptmm) REVERT: B 188 MET cc_start: 0.8797 (mmm) cc_final: 0.8495 (mmm) REVERT: B 234 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8896 (m-80) REVERT: B 335 PHE cc_start: 0.8537 (m-10) cc_final: 0.8155 (m-80) outliers start: 16 outliers final: 12 residues processed: 118 average time/residue: 1.0774 time to fit residues: 134.1866 Evaluate side-chains 110 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.109820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.086367 restraints weight = 13685.117| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.92 r_work: 0.3286 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6343 Z= 0.146 Angle : 0.655 9.566 8656 Z= 0.333 Chirality : 0.042 0.150 1042 Planarity : 0.004 0.054 1085 Dihedral : 3.885 18.384 894 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.85 % Allowed : 26.01 % Favored : 71.14 % 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: -0.11 (0.29), residues: 833 helix: 0.56 (0.28), residues: 330 sheet: -0.28 (0.38), residues: 178 loop : -0.44 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.007 0.001 HIS R 289 PHE 0.010 0.001 PHE B 292 TYR 0.016 0.002 TYR R 251 ARG 0.010 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03021 ( 293) hydrogen bonds : angle 4.50686 ( 828) SS BOND : bond 0.00250 ( 1) SS BOND : angle 1.06561 ( 2) covalent geometry : bond 0.00331 ( 6342) covalent geometry : angle 0.65506 ( 8654) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: R 68 TYR cc_start: 0.8595 (m-10) cc_final: 0.8344 (m-10) REVERT: R 158 PHE cc_start: 0.8151 (t80) cc_final: 0.7866 (t80) REVERT: R 295 ILE cc_start: 0.8807 (tp) cc_final: 0.8436 (pp) REVERT: B 57 LYS cc_start: 0.9144 (ptpp) cc_final: 0.8480 (ptmm) REVERT: B 188 MET cc_start: 0.8827 (mmm) cc_final: 0.8532 (mmm) REVERT: B 234 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.8919 (m-80) REVERT: B 335 PHE cc_start: 0.8559 (m-10) cc_final: 0.8181 (m-80) outliers start: 17 outliers final: 14 residues processed: 111 average time/residue: 1.0146 time to fit residues: 119.0191 Evaluate side-chains 109 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 66 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 0.0070 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.109785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.086430 restraints weight = 13772.302| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.94 r_work: 0.3289 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6343 Z= 0.140 Angle : 0.665 9.459 8656 Z= 0.339 Chirality : 0.042 0.151 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.943 18.398 894 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.02 % Allowed : 25.84 % Favored : 71.14 % 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: -0.16 (0.29), residues: 833 helix: 0.45 (0.28), residues: 332 sheet: -0.30 (0.38), residues: 178 loop : -0.40 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS R 289 PHE 0.009 0.001 PHE B 292 TYR 0.016 0.001 TYR R 307 ARG 0.011 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 293) hydrogen bonds : angle 4.58232 ( 828) SS BOND : bond 0.00009 ( 1) SS BOND : angle 1.01835 ( 2) covalent geometry : bond 0.00320 ( 6342) covalent geometry : angle 0.66515 ( 8654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4626.81 seconds wall clock time: 79 minutes 43.13 seconds (4783.13 seconds total)