Starting phenix.real_space_refine on Wed Feb 12 06:13:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f1s_31424/02_2025/7f1s_31424.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f1s_31424/02_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_31424/02_2025/7f1s_31424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f1s_31424/02_2025/7f1s_31424.map" model { file = "/net/cci-nas-00/data/ceres_data/7f1s_31424/02_2025/7f1s_31424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f1s_31424/02_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-5592/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: 4.23, per 1000 atoms: 0.68 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: 1.42 Conformation dependent library (CDL) restraints added in 928.2 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: 0.74 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: 1.99 Time building geometry restraints manager: 1.69 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: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.050 Find NCS groups from input model: 0.110 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.350 ------------------------------------------------------------------------------- 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 6342 Z= 0.125 Angle : 0.552 8.112 8654 Z= 0.289 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 *********************** 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 : 0.676 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: 1.0472 time to fit residues: 167.6869 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 : 0.727 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.115464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092185 restraints weight = 13437.098| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.05 r_work: 0.3396 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6342 Z= 0.233 Angle : 0.636 8.723 8654 Z= 0.326 Chirality : 0.043 0.145 1042 Planarity : 0.005 0.052 1085 Dihedral : 3.838 17.207 894 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: -0.53 (0.27), residues: 333 sheet: 0.60 (0.41), residues: 165 loop : -0.76 (0.34), residues: 335 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 0.001 PHE R 45 TYR 0.021 0.002 TYR R 307 ARG 0.008 0.001 ARG R 140 *********************** 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 : 0.757 Fit side-chains REVERT: R 110 ILE cc_start: 0.8854 (mp) cc_final: 0.8508 (mp) REVERT: R 197 LYS cc_start: 0.7953 (pttp) cc_final: 0.6651 (mmpt) REVERT: R 225 ARG cc_start: 0.7751 (ptm-80) cc_final: 0.7518 (ptm-80) REVERT: R 235 ARG cc_start: 0.7339 (tpt170) cc_final: 0.6991 (tpt170) REVERT: R 280 GLN cc_start: 0.8219 (tp-100) cc_final: 0.7991 (tp-100) REVERT: R 297 TYR cc_start: 0.9210 (m-80) cc_final: 0.8964 (m-80) REVERT: A 21 ARG cc_start: 0.8353 (ttp-110) cc_final: 0.8148 (ttp-110) REVERT: A 186 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7606 (mt-10) REVERT: A 230 TYR cc_start: 0.7821 (p90) cc_final: 0.7336 (p90) REVERT: A 304 GLN cc_start: 0.8815 (tt0) cc_final: 0.8541 (tt0) REVERT: B 188 MET cc_start: 0.9034 (mmm) cc_final: 0.8696 (mmm) REVERT: B 228 ASP cc_start: 0.8005 (p0) cc_final: 0.7690 (p0) REVERT: B 230 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.7985 (m110) outliers start: 14 outliers final: 6 residues processed: 130 average time/residue: 1.1130 time to fit residues: 152.1429 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 : 0.694 ------------------------------------------------------------------------------- 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: 0.9990 chunk 59 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.112615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.089156 restraints weight = 13556.277| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.03 r_work: 0.3339 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6342 Z= 0.247 Angle : 0.608 8.778 8654 Z= 0.313 Chirality : 0.043 0.175 1042 Planarity : 0.004 0.052 1085 Dihedral : 3.779 17.929 894 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.19 % Allowed : 17.45 % Favored : 79.36 % 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: -0.29 (0.29), residues: 833 helix: 0.08 (0.28), residues: 332 sheet: 0.51 (0.39), residues: 173 loop : -0.72 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS R 132 PHE 0.012 0.001 PHE B 222 TYR 0.015 0.001 TYR R 307 ARG 0.008 0.001 ARG R 140 *********************** 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 131 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 235 ARG cc_start: 0.7363 (tpt170) cc_final: 0.6871 (tpt170) REVERT: R 241 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8101 (mmt) REVERT: R 280 GLN cc_start: 0.8312 (tp-100) cc_final: 0.8011 (tp-100) REVERT: R 305 ARG cc_start: 0.7696 (mpp80) cc_final: 0.7423 (mmt90) REVERT: A 21 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.8222 (ttp-110) REVERT: A 186 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7645 (mt-10) REVERT: A 230 TYR cc_start: 0.7943 (p90) cc_final: 0.7543 (p90) REVERT: B 188 MET cc_start: 0.9041 (mmm) cc_final: 0.8692 (mmm) REVERT: B 228 ASP cc_start: 0.8139 (p0) cc_final: 0.7813 (p0) REVERT: B 230 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.7870 (m110) outliers start: 19 outliers final: 12 residues processed: 125 average time/residue: 1.0608 time to fit residues: 139.9855 Evaluate side-chains 110 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 208 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 B residue 118 ASP 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 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: 0.0980 chunk 55 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.110891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.087315 restraints weight = 13748.457| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.03 r_work: 0.3301 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6342 Z= 0.236 Angle : 0.596 8.842 8654 Z= 0.307 Chirality : 0.042 0.150 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.762 18.406 894 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.52 % Allowed : 19.97 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.29), residues: 833 helix: 0.40 (0.28), residues: 335 sheet: 0.32 (0.39), residues: 173 loop : -0.78 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 132 PHE 0.009 0.001 PHE B 222 TYR 0.018 0.002 TYR R 297 ARG 0.007 0.001 ARG A 32 *********************** 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 131 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: R 100 MET cc_start: 0.6322 (tmm) cc_final: 0.5785 (tmm) REVERT: R 235 ARG cc_start: 0.7388 (tpt170) cc_final: 0.6839 (tpt170) REVERT: R 241 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8122 (mmt) REVERT: R 305 ARG cc_start: 0.7753 (mpp80) cc_final: 0.7445 (mmt90) REVERT: A 18 MET cc_start: 0.8286 (mmt) cc_final: 0.8068 (mmt) REVERT: A 21 ARG cc_start: 0.8434 (ttp-110) cc_final: 0.8188 (ttp-110) REVERT: A 186 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7789 (mt-10) REVERT: A 230 TYR cc_start: 0.7799 (p90) cc_final: 0.7493 (p90) REVERT: B 78 LYS cc_start: 0.8809 (mptp) cc_final: 0.8590 (mmtm) REVERT: B 188 MET cc_start: 0.9023 (mmm) cc_final: 0.8655 (mmm) outliers start: 21 outliers final: 17 residues processed: 123 average time/residue: 1.0318 time to fit residues: 134.0216 Evaluate side-chains 118 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 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 76 ASP 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 Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.110837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.087466 restraints weight = 13605.335| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.91 r_work: 0.3307 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6342 Z= 0.213 Angle : 0.590 8.910 8654 Z= 0.304 Chirality : 0.042 0.147 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.789 18.480 894 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.52 % Allowed : 20.81 % Favored : 75.67 % 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: 0.49 (0.28), residues: 335 sheet: 0.24 (0.39), residues: 173 loop : -0.73 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS R 132 PHE 0.008 0.001 PHE A 196 TYR 0.018 0.002 TYR R 297 ARG 0.007 0.001 ARG A 32 *********************** 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 127 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.734 Fit side-chains REVERT: R 235 ARG cc_start: 0.7386 (tpt170) cc_final: 0.6888 (tpt170) REVERT: R 241 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8124 (mmt) REVERT: R 305 ARG cc_start: 0.7845 (mpp80) cc_final: 0.7492 (mmt90) REVERT: A 18 MET cc_start: 0.8272 (mmt) cc_final: 0.8022 (mmt) REVERT: A 21 ARG cc_start: 0.8418 (ttp-110) cc_final: 0.8189 (ttp-110) REVERT: A 186 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7782 (mt-10) REVERT: A 230 TYR cc_start: 0.7696 (p90) cc_final: 0.7494 (p90) REVERT: B 188 MET cc_start: 0.8985 (mmm) cc_final: 0.8705 (mmm) REVERT: B 260 GLU cc_start: 0.7544 (tp30) cc_final: 0.7211 (tp30) outliers start: 21 outliers final: 14 residues processed: 117 average time/residue: 1.0700 time to fit residues: 132.2318 Evaluate side-chains 111 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.110528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.087153 restraints weight = 13456.631| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.89 r_work: 0.3300 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6342 Z= 0.209 Angle : 0.591 9.404 8654 Z= 0.304 Chirality : 0.041 0.147 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.753 18.420 894 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.36 % Allowed : 22.65 % Favored : 73.99 % 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: -0.06 (0.29), residues: 833 helix: 0.60 (0.29), residues: 332 sheet: 0.19 (0.39), residues: 173 loop : -0.72 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS R 132 PHE 0.007 0.001 PHE A 196 TYR 0.017 0.002 TYR R 297 ARG 0.008 0.001 ARG A 32 *********************** 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 127 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: R 100 MET cc_start: 0.6256 (tmm) cc_final: 0.5651 (tmm) REVERT: R 235 ARG cc_start: 0.7465 (tpt170) cc_final: 0.6886 (tpt170) REVERT: R 241 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8119 (mmt) REVERT: R 305 ARG cc_start: 0.7904 (mpp80) cc_final: 0.7522 (mmt90) REVERT: A 18 MET cc_start: 0.8361 (mmt) cc_final: 0.8116 (mmt) REVERT: A 21 ARG cc_start: 0.8437 (ttp-110) cc_final: 0.8219 (ttp-110) REVERT: A 186 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7821 (mt-10) REVERT: B 188 MET cc_start: 0.8972 (mmm) cc_final: 0.8673 (mmm) outliers start: 20 outliers final: 14 residues processed: 119 average time/residue: 1.0385 time to fit residues: 130.6568 Evaluate side-chains 113 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 110 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.107287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.083675 restraints weight = 13561.686| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.85 r_work: 0.3233 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6342 Z= 0.296 Angle : 0.652 9.510 8654 Z= 0.339 Chirality : 0.043 0.149 1042 Planarity : 0.004 0.055 1085 Dihedral : 3.993 19.686 894 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.02 % Allowed : 24.50 % Favored : 72.48 % 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: -0.06 (0.29), residues: 833 helix: 0.58 (0.28), residues: 334 sheet: -0.05 (0.39), residues: 176 loop : -0.53 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.003 0.001 HIS B 91 PHE 0.018 0.001 PHE B 292 TYR 0.015 0.002 TYR R 307 ARG 0.005 0.001 ARG A 32 *********************** 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 121 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.722 Fit side-chains REVERT: R 158 PHE cc_start: 0.8175 (t80) cc_final: 0.7885 (t80) REVERT: R 235 ARG cc_start: 0.7456 (tpt170) cc_final: 0.7083 (tpt170) REVERT: R 241 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8168 (mmt) REVERT: R 305 ARG cc_start: 0.7958 (mpp80) cc_final: 0.7741 (mmt90) REVERT: A 18 MET cc_start: 0.8322 (mmt) cc_final: 0.8084 (mmt) REVERT: A 186 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7905 (mt-10) REVERT: B 188 MET cc_start: 0.8977 (mmm) cc_final: 0.8694 (mmm) outliers start: 18 outliers final: 14 residues processed: 115 average time/residue: 1.0680 time to fit residues: 129.6723 Evaluate side-chains 108 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 34 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN A 255 ASN A 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.108271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.084863 restraints weight = 13525.567| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.89 r_work: 0.3255 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6342 Z= 0.236 Angle : 0.639 9.088 8654 Z= 0.330 Chirality : 0.042 0.151 1042 Planarity : 0.004 0.054 1085 Dihedral : 3.965 19.596 894 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.02 % Allowed : 26.34 % Favored : 70.64 % 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: -0.07 (0.29), residues: 833 helix: 0.59 (0.28), residues: 333 sheet: -0.06 (0.39), residues: 174 loop : -0.55 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS R 132 PHE 0.009 0.001 PHE A 196 TYR 0.016 0.002 TYR R 307 ARG 0.008 0.001 ARG A 32 *********************** 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 113 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.660 Fit side-chains REVERT: R 68 TYR cc_start: 0.8494 (m-80) cc_final: 0.8283 (m-10) REVERT: R 158 PHE cc_start: 0.8157 (t80) cc_final: 0.7856 (t80) REVERT: R 235 ARG cc_start: 0.7511 (tpt170) cc_final: 0.7176 (tpt170) REVERT: R 241 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8146 (mmt) REVERT: R 305 ARG cc_start: 0.7982 (mpp80) cc_final: 0.7760 (mmt90) REVERT: A 18 MET cc_start: 0.8297 (mmt) cc_final: 0.8071 (mmt) REVERT: A 21 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.8278 (ttp-110) REVERT: B 188 MET cc_start: 0.8956 (mmm) cc_final: 0.8632 (mmm) outliers start: 18 outliers final: 12 residues processed: 108 average time/residue: 1.1328 time to fit residues: 129.0934 Evaluate side-chains 106 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 76 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 142 HIS B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.109921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.086686 restraints weight = 13664.044| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.90 r_work: 0.3290 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6342 Z= 0.190 Angle : 0.632 9.328 8654 Z= 0.325 Chirality : 0.042 0.150 1042 Planarity : 0.004 0.054 1085 Dihedral : 3.909 18.928 894 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.35 % Allowed : 26.17 % Favored : 71.48 % 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: 0.00 (0.29), residues: 833 helix: 0.64 (0.28), residues: 331 sheet: -0.03 (0.39), residues: 172 loop : -0.49 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 132 PHE 0.011 0.001 PHE B 292 TYR 0.017 0.001 TYR R 297 ARG 0.009 0.001 ARG A 32 *********************** 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 112 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: R 68 TYR cc_start: 0.8435 (m-10) cc_final: 0.8225 (m-10) REVERT: R 158 PHE cc_start: 0.8143 (t80) cc_final: 0.7841 (t80) REVERT: R 235 ARG cc_start: 0.7433 (tpt170) cc_final: 0.7140 (tpt170) REVERT: R 241 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8125 (mmt) REVERT: R 305 ARG cc_start: 0.7978 (mpp80) cc_final: 0.7741 (mmt90) REVERT: A 18 MET cc_start: 0.8290 (mmt) cc_final: 0.8071 (mmt) REVERT: A 21 ARG cc_start: 0.8493 (ttp-110) cc_final: 0.8262 (ttp-110) REVERT: B 188 MET cc_start: 0.8908 (mmm) cc_final: 0.8602 (mmm) outliers start: 14 outliers final: 11 residues processed: 107 average time/residue: 1.1626 time to fit residues: 130.7612 Evaluate side-chains 107 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 125 ASP 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 196 THR 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 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 0.0770 chunk 72 optimal weight: 0.4980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.109758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.086489 restraints weight = 13712.992| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.91 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: 0.7959 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6342 Z= 0.201 Angle : 0.651 9.434 8654 Z= 0.335 Chirality : 0.042 0.181 1042 Planarity : 0.004 0.054 1085 Dihedral : 3.893 18.846 894 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.52 % Allowed : 26.51 % Favored : 70.97 % 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: 0.00 (0.29), residues: 833 helix: 0.66 (0.28), residues: 331 sheet: -0.14 (0.39), residues: 174 loop : -0.44 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 132 PHE 0.008 0.001 PHE A 196 TYR 0.016 0.002 TYR R 251 ARG 0.008 0.001 ARG A 32 ********************** 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 113 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: R 100 MET cc_start: 0.6128 (pp-130) cc_final: 0.5126 (tmm) REVERT: R 126 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8832 (mtt-85) REVERT: R 158 PHE cc_start: 0.8137 (t80) cc_final: 0.7834 (t80) REVERT: R 210 MET cc_start: 0.9131 (mtt) cc_final: 0.8877 (mtt) REVERT: R 225 ARG cc_start: 0.8335 (tmm160) cc_final: 0.8115 (ttp-170) REVERT: R 235 ARG cc_start: 0.7321 (tpt170) cc_final: 0.7120 (tpt170) REVERT: R 241 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8113 (mmt) REVERT: R 305 ARG cc_start: 0.7985 (mpp80) cc_final: 0.7745 (mmt90) REVERT: A 21 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.8265 (ttp-110) REVERT: B 57 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8328 (ptmm) outliers start: 15 outliers final: 11 residues processed: 110 average time/residue: 1.1223 time to fit residues: 130.0669 Evaluate side-chains 108 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 125 ASP Chi-restraints excluded: chain R residue 126 ARG 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 57 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 74 optimal weight: 0.0040 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 0.0870 chunk 69 optimal weight: 0.4980 overall best weight: 0.4972 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.110098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.086644 restraints weight = 13771.786| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.94 r_work: 0.3292 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6342 Z= 0.197 Angle : 0.667 13.440 8654 Z= 0.339 Chirality : 0.042 0.178 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.867 18.703 894 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.52 % Allowed : 25.84 % Favored : 70.64 % 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: 0.02 (0.29), residues: 833 helix: 0.62 (0.28), residues: 333 sheet: -0.12 (0.39), residues: 174 loop : -0.38 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 132 PHE 0.008 0.001 PHE A 196 TYR 0.016 0.001 TYR R 307 ARG 0.008 0.001 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4484.39 seconds wall clock time: 79 minutes 53.59 seconds (4793.59 seconds total)