Starting phenix.real_space_refine on Tue Aug 4 23:34:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w2g_65570/08_2026/9w2g_65570.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w2g_65570/08_2026/9w2g_65570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w2g_65570/08_2026/9w2g_65570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w2g_65570/08_2026/9w2g_65570.map" model { file = "/net/cci-nas-00/data/ceres_data/9w2g_65570/08_2026/9w2g_65570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w2g_65570/08_2026/9w2g_65570.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 4689 2.51 5 N 1235 2.21 5 O 1273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7250 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 241 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1540 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 63 Chain: "N" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 847 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2249 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2315 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 7, 'ASP:plan': 13, 'ASN:plan1': 5, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 117 Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Classifications: {'peptide': 7} Link IDs: {'CIS': 1, 'NMTRANS': 1, 'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'MLE:plan-1': 1, 'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.51, per 1000 atoms: 0.21 Number of scatterers: 7250 At special positions: 0 Unit cell: (73.61, 97.425, 128.817, 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 53 16.00 O 1273 8.00 N 1235 7.00 C 4689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 181 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 353.3 milliseconds 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 39.4% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'G' and resid 13 through 23 removed outlier: 4.378A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'A' and resid 26 through 40 removed outlier: 3.619A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.724A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.685A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.826A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.939A pdb=" N ALA A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 317' Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.723A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.745A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.536A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 29 through 61 removed outlier: 5.099A pdb=" N LEU R 35 " --> pdb=" O TRP R 31 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP R 36 " --> pdb=" O GLN R 32 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS R 61 " --> pdb=" O ILE R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 95 Processing helix chain 'R' and resid 105 through 110 removed outlier: 3.619A pdb=" N ASN R 110 " --> pdb=" O CYS R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 133 Processing helix chain 'R' and resid 144 through 164 Processing helix chain 'R' and resid 165 through 167 No H-bonds generated for 'chain 'R' and resid 165 through 167' Processing helix chain 'R' and resid 191 through 206 removed outlier: 3.522A pdb=" N LEU R 195 " --> pdb=" O GLY R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 227 Processing helix chain 'R' and resid 241 through 263 removed outlier: 4.161A pdb=" N MET R 245 " --> pdb=" O HIS R 241 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU R 254 " --> pdb=" O LYS R 250 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE R 261 " --> pdb=" O LEU R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 272 removed outlier: 3.816A pdb=" N HIS R 267 " --> pdb=" O TRP R 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE R 270 " --> pdb=" O TYR R 266 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE R 271 " --> pdb=" O HIS R 267 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU R 272 " --> pdb=" O LEU R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 298 removed outlier: 4.520A pdb=" N GLN R 287 " --> pdb=" O LYS R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 312 removed outlier: 3.620A pdb=" N TYR R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN R 303 " --> pdb=" O SER R 299 " (cutoff:3.500A) Proline residue: R 304 - end of helix removed outlier: 3.615A pdb=" N CYS R 308 " --> pdb=" O PRO R 304 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N CYS R 309 " --> pdb=" O ILE R 305 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU R 310 " --> pdb=" O ILE R 306 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN R 311 " --> pdb=" O TYR R 307 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N HIS R 312 " --> pdb=" O CYS R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 321 Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 29 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 3.537A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.557A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.025A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET N 34 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR N 94 " --> pdb=" O THR N 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.658A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.872A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.679A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.809A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.612A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.818A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.632A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 936 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: 0.87 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1115 1.29 - 1.42: 2084 1.42 - 1.55: 4136 1.55 - 1.68: 8 1.68 - 1.81: 75 Bond restraints: 7418 Sorted by residual: bond pdb=" C MLE C 6 " pdb=" N NLE C 7 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.83e+02 bond pdb=" C GLY C 5 " pdb=" N MLE C 6 " ideal model delta sigma weight residual 1.329 1.507 -0.178 1.40e-02 5.10e+03 1.62e+02 bond pdb=" C LYS C 2 " pdb=" N TYR C 3 " ideal model delta sigma weight residual 1.329 1.486 -0.157 1.40e-02 5.10e+03 1.26e+02 bond pdb=" C ASP C 1 " pdb=" N LYS C 2 " ideal model delta sigma weight residual 1.332 1.476 -0.144 1.40e-02 5.10e+03 1.05e+02 bond pdb=" C VAL C 4 " pdb=" N GLY C 5 " ideal model delta sigma weight residual 1.329 1.470 -0.141 1.40e-02 5.10e+03 1.02e+02 ... (remaining 7413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 10066 3.99 - 7.98: 36 7.98 - 11.97: 5 11.97 - 15.96: 4 15.96 - 19.95: 1 Bond angle restraints: 10112 Sorted by residual: angle pdb=" N TYR C 3 " pdb=" CA TYR C 3 " pdb=" CB TYR C 3 " ideal model delta sigma weight residual 110.50 124.21 -13.71 1.70e+00 3.46e-01 6.51e+01 angle pdb=" C LYS C 2 " pdb=" N TYR C 3 " pdb=" CA TYR C 3 " ideal model delta sigma weight residual 121.70 135.73 -14.03 1.80e+00 3.09e-01 6.07e+01 angle pdb=" CA TYR C 3 " pdb=" CB TYR C 3 " pdb=" CG TYR C 3 " ideal model delta sigma weight residual 113.90 100.53 13.37 1.80e+00 3.09e-01 5.52e+01 angle pdb=" C TYR C 3 " pdb=" N VAL C 4 " pdb=" CA VAL C 4 " ideal model delta sigma weight residual 122.58 112.53 10.05 1.48e+00 4.57e-01 4.61e+01 angle pdb=" CA NLE C 7 " pdb=" CB NLE C 7 " pdb=" CG NLE C 7 " ideal model delta sigma weight residual 114.27 134.22 -19.95 3.00e+00 1.11e-01 4.42e+01 ... (remaining 10107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3696 17.94 - 35.88: 447 35.88 - 53.82: 124 53.82 - 71.76: 10 71.76 - 89.69: 6 Dihedral angle restraints: 4283 sinusoidal: 1458 harmonic: 2825 Sorted by residual: dihedral pdb=" C TYR C 3 " pdb=" N TYR C 3 " pdb=" CA TYR C 3 " pdb=" CB TYR C 3 " ideal model delta harmonic sigma weight residual -122.60 -109.55 -13.05 0 2.50e+00 1.60e-01 2.73e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -154.33 -25.67 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -156.02 -23.98 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 4280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 944 0.053 - 0.105: 177 0.105 - 0.158: 49 0.158 - 0.211: 7 0.211 - 0.263: 2 Chirality restraints: 1179 Sorted by residual: chirality pdb=" CA LYS C 2 " pdb=" N LYS C 2 " pdb=" C LYS C 2 " pdb=" CB LYS C 2 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB THR N 111 " pdb=" CA THR N 111 " pdb=" OG1 THR N 111 " pdb=" CG2 THR N 111 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB VAL C 4 " pdb=" CA VAL C 4 " pdb=" CG1 VAL C 4 " pdb=" CG2 VAL C 4 " both_signs ideal model delta sigma weight residual False -2.63 -2.84 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1176 not shown) Planarity restraints: 1259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 197 " 0.017 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C TYR R 197 " -0.062 2.00e-02 2.50e+03 pdb=" O TYR R 197 " 0.024 2.00e-02 2.50e+03 pdb=" N HIS R 198 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 131 " -0.279 9.50e-02 1.11e+02 1.25e-01 9.65e+00 pdb=" NE ARG R 131 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG R 131 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG R 131 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG R 131 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS R 198 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.52e+00 pdb=" C HIS R 198 " -0.053 2.00e-02 2.50e+03 pdb=" O HIS R 198 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU R 199 " 0.019 2.00e-02 2.50e+03 ... (remaining 1256 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1286 2.76 - 3.30: 6700 3.30 - 3.83: 11972 3.83 - 4.37: 13166 4.37 - 4.90: 24003 Nonbonded interactions: 57127 Sorted by model distance: nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.230 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.245 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.272 3.040 nonbonded pdb=" O LYS B 57 " pdb=" OG SER B 74 " model vdw 2.295 3.040 nonbonded pdb=" NH2 ARG A 231 " pdb=" OD1 ASP A 272 " model vdw 2.299 3.120 ... (remaining 57122 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 : 0.006 0.189 7422 Z= 0.408 Angle : 0.758 19.948 10118 Z= 0.428 Chirality : 0.047 0.263 1179 Planarity : 0.005 0.125 1259 Dihedral : 16.837 89.694 2444 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.12 % Favored : 94.77 % Rotamer: Outliers : 1.00 % Allowed : 29.91 % Favored : 69.09 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.29), residues: 937 helix: 1.34 (0.31), residues: 303 sheet: -0.14 (0.37), residues: 213 loop : -0.81 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 131 TYR 0.022 0.001 TYR C 3 PHE 0.009 0.001 PHE R 91 TRP 0.021 0.001 TRP A 281 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.41 ( 7418) covalent geometry : angle 0.75703 / 0.43 (10112) SS BOND : bond 0.00239 / 0.12 ( 3) SS BOND : angle 1.53528 / 0.75 ( 6) hydrogen bonds : bond 0.20855 / 14.46 ( 329) hydrogen bonds : angle 7.14276 / 5.08 ( 936) Misc. bond : bond 0.00322 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.285 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 140 average time/residue: 0.0742 time to fit residues: 14.7299 Evaluate side-chains 136 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 2 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0770 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.175298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.139668 restraints weight = 8114.728| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.72 r_work: 0.3567 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7422 Z= 0.195 Angle : 0.623 8.477 10118 Z= 0.333 Chirality : 0.046 0.165 1179 Planarity : 0.005 0.067 1259 Dihedral : 5.249 46.172 1045 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 6.41 % Allowed : 25.07 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.29), residues: 937 helix: 1.08 (0.29), residues: 328 sheet: -0.47 (0.35), residues: 224 loop : -1.05 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 227 TYR 0.016 0.002 TYR C 3 PHE 0.015 0.002 PHE R 118 TRP 0.020 0.002 TRP R 263 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 ( 7418) covalent geometry : angle 0.62048 / 0.33 (10112) SS BOND : bond 0.00357 / 0.18 ( 3) SS BOND : angle 2.15843 / 1.14 ( 6) hydrogen bonds : bond 0.04388 / 3.00 ( 329) hydrogen bonds : angle 5.22361 / 3.77 ( 936) Misc. bond : bond 0.00082 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8212 (t0) cc_final: 0.7982 (t0) REVERT: A 293 LYS cc_start: 0.8816 (pttp) cc_final: 0.8506 (pttt) REVERT: R 124 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.6424 (mtt) REVERT: R 213 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7481 (ttp) REVERT: R 284 PHE cc_start: 0.6264 (OUTLIER) cc_final: 0.5972 (t80) outliers start: 45 outliers final: 25 residues processed: 184 average time/residue: 0.0699 time to fit residues: 17.8213 Evaluate side-chains 172 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 284 PHE Chi-restraints excluded: chain R residue 285 ILE Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain R residue 315 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain C residue 1 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 198 HIS ** R 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.176991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.141332 restraints weight = 7990.544| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.74 r_work: 0.3581 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7422 Z= 0.150 Angle : 0.576 8.417 10118 Z= 0.303 Chirality : 0.044 0.183 1179 Planarity : 0.004 0.063 1259 Dihedral : 4.933 40.015 1040 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 6.27 % Allowed : 26.92 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.28), residues: 937 helix: 1.16 (0.29), residues: 328 sheet: -0.49 (0.35), residues: 220 loop : -1.03 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 227 TYR 0.017 0.002 TYR C 3 PHE 0.015 0.001 PHE B 199 TRP 0.016 0.002 TRP R 263 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 7418) covalent geometry : angle 0.57355 / 0.30 (10112) SS BOND : bond 0.00385 / 0.18 ( 3) SS BOND : angle 2.14660 / 1.10 ( 6) hydrogen bonds : bond 0.03994 / 2.75 ( 329) hydrogen bonds : angle 4.85298 / 3.49 ( 936) Misc. bond : bond 0.00074 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8865 (tp40) cc_final: 0.8641 (tp-100) REVERT: A 223 ASP cc_start: 0.8033 (t0) cc_final: 0.7744 (t0) REVERT: A 281 TRP cc_start: 0.7825 (m100) cc_final: 0.7355 (m100) REVERT: A 293 LYS cc_start: 0.8693 (pttp) cc_final: 0.8429 (pttt) REVERT: A 302 LEU cc_start: 0.8805 (mt) cc_final: 0.8277 (pp) REVERT: R 100 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.5842 (m-80) REVERT: R 284 PHE cc_start: 0.6124 (OUTLIER) cc_final: 0.5924 (t80) REVERT: B 188 MET cc_start: 0.8531 (mmm) cc_final: 0.8216 (mmm) outliers start: 44 outliers final: 25 residues processed: 177 average time/residue: 0.0679 time to fit residues: 17.1284 Evaluate side-chains 168 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 284 PHE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain C residue 1 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 30 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.179128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.143316 restraints weight = 8004.018| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.76 r_work: 0.3603 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7422 Z= 0.120 Angle : 0.551 7.763 10118 Z= 0.287 Chirality : 0.044 0.197 1179 Planarity : 0.004 0.061 1259 Dihedral : 4.545 27.092 1040 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.27 % Allowed : 27.64 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.28), residues: 937 helix: 1.42 (0.29), residues: 326 sheet: -0.45 (0.36), residues: 206 loop : -1.05 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 227 TYR 0.012 0.001 TYR A 318 PHE 0.014 0.001 PHE B 199 TRP 0.012 0.001 TRP R 99 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 7418) covalent geometry : angle 0.54930 / 0.29 (10112) SS BOND : bond 0.00330 / 0.16 ( 3) SS BOND : angle 1.87852 / 0.97 ( 6) hydrogen bonds : bond 0.03559 / 2.49 ( 329) hydrogen bonds : angle 4.59127 / 3.30 ( 936) Misc. bond : bond 0.00049 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8854 (tp40) cc_final: 0.8620 (tp-100) REVERT: A 281 TRP cc_start: 0.7740 (m100) cc_final: 0.7310 (m100) REVERT: A 293 LYS cc_start: 0.8664 (pttp) cc_final: 0.8430 (pttt) REVERT: A 302 LEU cc_start: 0.8751 (mt) cc_final: 0.8263 (pp) REVERT: R 100 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.5893 (m-80) REVERT: R 213 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7488 (mtm) REVERT: R 284 PHE cc_start: 0.6171 (OUTLIER) cc_final: 0.5951 (t80) REVERT: B 234 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.6586 (m-80) outliers start: 44 outliers final: 29 residues processed: 178 average time/residue: 0.0654 time to fit residues: 16.5594 Evaluate side-chains 181 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 284 PHE Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 1 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 93 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.177263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141368 restraints weight = 8036.510| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.73 r_work: 0.3590 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7422 Z= 0.134 Angle : 0.559 8.169 10118 Z= 0.292 Chirality : 0.044 0.207 1179 Planarity : 0.004 0.062 1259 Dihedral : 4.486 25.983 1040 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 7.55 % Allowed : 26.92 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.28), residues: 937 helix: 1.34 (0.29), residues: 329 sheet: -0.47 (0.35), residues: 212 loop : -1.02 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 227 TYR 0.017 0.001 TYR C 3 PHE 0.016 0.001 PHE B 199 TRP 0.010 0.001 TRP R 99 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 7418) covalent geometry : angle 0.55722 / 0.29 (10112) SS BOND : bond 0.00255 / 0.12 ( 3) SS BOND : angle 1.73756 / 0.87 ( 6) hydrogen bonds : bond 0.03587 / 2.50 ( 329) hydrogen bonds : angle 4.55820 / 3.29 ( 936) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 150 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8849 (tp40) cc_final: 0.8580 (tp-100) REVERT: A 281 TRP cc_start: 0.7737 (m100) cc_final: 0.7360 (m100) REVERT: A 302 LEU cc_start: 0.8684 (mt) cc_final: 0.8165 (pp) REVERT: A 343 ASP cc_start: 0.7945 (m-30) cc_final: 0.7216 (m-30) REVERT: R 100 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.5822 (m-80) REVERT: R 124 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6603 (mtm) REVERT: R 213 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7558 (mtm) REVERT: R 275 PHE cc_start: 0.5875 (OUTLIER) cc_final: 0.5585 (t80) REVERT: R 284 PHE cc_start: 0.6217 (OUTLIER) cc_final: 0.5997 (t80) REVERT: B 201 SER cc_start: 0.8681 (m) cc_final: 0.8393 (p) REVERT: B 234 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.6734 (m-80) outliers start: 53 outliers final: 38 residues processed: 187 average time/residue: 0.0686 time to fit residues: 18.2368 Evaluate side-chains 187 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 284 PHE Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.176921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.141066 restraints weight = 8061.279| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.74 r_work: 0.3584 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7422 Z= 0.142 Angle : 0.569 7.705 10118 Z= 0.296 Chirality : 0.044 0.220 1179 Planarity : 0.004 0.061 1259 Dihedral : 4.465 25.834 1038 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 7.69 % Allowed : 26.78 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.28), residues: 937 helix: 1.36 (0.30), residues: 329 sheet: -0.46 (0.35), residues: 210 loop : -1.02 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 227 TYR 0.016 0.001 TYR C 3 PHE 0.015 0.001 PHE B 199 TRP 0.011 0.001 TRP A 281 HIS 0.004 0.001 HIS R 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 7418) covalent geometry : angle 0.56695 / 0.29 (10112) SS BOND : bond 0.00329 / 0.16 ( 3) SS BOND : angle 1.86040 / 0.94 ( 6) hydrogen bonds : bond 0.03588 / 2.49 ( 329) hydrogen bonds : angle 4.52705 / 3.28 ( 936) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 151 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8865 (tp40) cc_final: 0.8551 (tp-100) REVERT: A 302 LEU cc_start: 0.8532 (mt) cc_final: 0.8052 (pp) REVERT: A 343 ASP cc_start: 0.7923 (m-30) cc_final: 0.7203 (m-30) REVERT: R 100 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.5899 (m-80) REVERT: R 213 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7601 (mtm) REVERT: R 275 PHE cc_start: 0.5906 (OUTLIER) cc_final: 0.5663 (t80) REVERT: B 59 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8353 (t80) REVERT: B 234 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.6627 (m-80) outliers start: 54 outliers final: 37 residues processed: 187 average time/residue: 0.0679 time to fit residues: 17.9892 Evaluate side-chains 187 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 285 ILE Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.177450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.140614 restraints weight = 8044.471| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.82 r_work: 0.3574 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7422 Z= 0.141 Angle : 0.571 8.294 10118 Z= 0.297 Chirality : 0.044 0.229 1179 Planarity : 0.004 0.061 1259 Dihedral : 4.512 29.983 1038 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 7.12 % Allowed : 27.92 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.28), residues: 937 helix: 1.36 (0.30), residues: 329 sheet: -0.46 (0.35), residues: 209 loop : -1.02 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 227 TYR 0.015 0.001 TYR C 3 PHE 0.014 0.001 PHE B 199 TRP 0.013 0.001 TRP R 99 HIS 0.004 0.001 HIS R 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 7418) covalent geometry : angle 0.56945 / 0.30 (10112) SS BOND : bond 0.00294 / 0.14 ( 3) SS BOND : angle 1.81355 / 0.94 ( 6) hydrogen bonds : bond 0.03608 / 2.51 ( 329) hydrogen bonds : angle 4.51944 / 3.27 ( 936) Misc. bond : bond 0.00067 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7863 (mp10) REVERT: A 31 GLN cc_start: 0.8879 (tp40) cc_final: 0.8563 (tp-100) REVERT: A 302 LEU cc_start: 0.8504 (mt) cc_final: 0.8026 (pp) REVERT: A 343 ASP cc_start: 0.7971 (m-30) cc_final: 0.7202 (m-30) REVERT: R 100 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.5895 (m-80) REVERT: R 124 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6644 (mtm) REVERT: R 213 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7608 (mtm) REVERT: R 275 PHE cc_start: 0.5827 (OUTLIER) cc_final: 0.5587 (t80) REVERT: B 59 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8383 (t80) REVERT: B 234 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.6687 (m-80) outliers start: 50 outliers final: 36 residues processed: 182 average time/residue: 0.0620 time to fit residues: 16.0554 Evaluate side-chains 186 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 285 ILE Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 60 optimal weight: 0.0970 chunk 67 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.178791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.142595 restraints weight = 8044.911| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.73 r_work: 0.3601 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7422 Z= 0.128 Angle : 0.564 8.068 10118 Z= 0.292 Chirality : 0.044 0.242 1179 Planarity : 0.004 0.071 1259 Dihedral : 4.440 30.046 1038 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 6.27 % Allowed : 28.35 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.28), residues: 937 helix: 1.36 (0.30), residues: 329 sheet: -0.45 (0.35), residues: 210 loop : -0.99 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG R 227 TYR 0.013 0.001 TYR C 3 PHE 0.015 0.001 PHE B 199 TRP 0.012 0.001 TRP R 99 HIS 0.004 0.001 HIS R 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7418) covalent geometry : angle 0.56303 / 0.29 (10112) SS BOND : bond 0.00311 / 0.15 ( 3) SS BOND : angle 1.75355 / 0.88 ( 6) hydrogen bonds : bond 0.03517 / 2.45 ( 329) hydrogen bonds : angle 4.45961 / 3.23 ( 936) Misc. bond : bond 0.00053 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7859 (mp10) REVERT: A 31 GLN cc_start: 0.8877 (tp40) cc_final: 0.8562 (tp-100) REVERT: A 302 LEU cc_start: 0.8495 (mt) cc_final: 0.8041 (pp) REVERT: A 343 ASP cc_start: 0.7960 (m-30) cc_final: 0.7294 (m-30) REVERT: A 357 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7761 (p-80) REVERT: R 100 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.5886 (m-80) REVERT: R 213 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7543 (mtm) REVERT: R 275 PHE cc_start: 0.5807 (OUTLIER) cc_final: 0.5590 (t80) REVERT: B 59 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8273 (t80) REVERT: B 234 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.6534 (m-80) outliers start: 44 outliers final: 32 residues processed: 178 average time/residue: 0.0647 time to fit residues: 16.4070 Evaluate side-chains 180 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 75 optimal weight: 0.0030 chunk 90 optimal weight: 5.9990 chunk 27 optimal weight: 0.0170 chunk 31 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.3228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.182958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147383 restraints weight = 7883.874| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.71 r_work: 0.3658 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7422 Z= 0.104 Angle : 0.554 8.676 10118 Z= 0.281 Chirality : 0.043 0.248 1179 Planarity : 0.004 0.084 1259 Dihedral : 4.147 26.125 1038 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.56 % Allowed : 29.77 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.28), residues: 937 helix: 1.46 (0.30), residues: 328 sheet: -0.29 (0.34), residues: 209 loop : -1.00 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG R 227 TYR 0.010 0.001 TYR A 339 PHE 0.015 0.001 PHE B 199 TRP 0.015 0.001 TRP R 263 HIS 0.004 0.001 HIS R 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 7418) covalent geometry : angle 0.55285 / 0.28 (10112) SS BOND : bond 0.00237 / 0.12 ( 3) SS BOND : angle 1.43682 / 0.71 ( 6) hydrogen bonds : bond 0.03217 / 2.25 ( 329) hydrogen bonds : angle 4.29386 / 3.10 ( 936) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7879 (mp10) REVERT: A 31 GLN cc_start: 0.8851 (tp40) cc_final: 0.8565 (tp-100) REVERT: A 357 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7671 (p-80) REVERT: R 100 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.5760 (m-80) REVERT: R 213 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7398 (mtm) REVERT: B 59 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8294 (t80) REVERT: B 188 MET cc_start: 0.8370 (mmm) cc_final: 0.8043 (mmm) REVERT: B 234 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.6363 (m-80) REVERT: B 297 TRP cc_start: 0.7850 (m100) cc_final: 0.7393 (m100) outliers start: 32 outliers final: 21 residues processed: 169 average time/residue: 0.0578 time to fit residues: 13.7725 Evaluate side-chains 172 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 64 optimal weight: 0.0070 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.182884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.147094 restraints weight = 7883.470| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.69 r_work: 0.3650 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7422 Z= 0.114 Angle : 0.577 9.042 10118 Z= 0.292 Chirality : 0.044 0.266 1179 Planarity : 0.005 0.103 1259 Dihedral : 4.168 27.500 1038 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.99 % Allowed : 30.06 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.28), residues: 937 helix: 1.51 (0.30), residues: 328 sheet: -0.26 (0.34), residues: 209 loop : -0.97 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG R 227 TYR 0.014 0.001 TYR A 339 PHE 0.014 0.001 PHE B 199 TRP 0.013 0.001 TRP R 99 HIS 0.004 0.001 HIS R 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 7418) covalent geometry : angle 0.57638 / 0.29 (10112) SS BOND : bond 0.00251 / 0.12 ( 3) SS BOND : angle 1.49556 / 0.74 ( 6) hydrogen bonds : bond 0.03246 / 2.26 ( 329) hydrogen bonds : angle 4.29270 / 3.11 ( 936) Misc. bond : bond 0.00032 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1874 Ramachandran restraints generated. 937 Oldfield, 0 Emsley, 937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7923 (mp10) REVERT: A 31 GLN cc_start: 0.8857 (tp40) cc_final: 0.8566 (tp-100) REVERT: A 357 HIS cc_start: 0.7934 (OUTLIER) cc_final: 0.7572 (p-80) REVERT: R 100 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.5757 (m-80) REVERT: R 205 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7277 (pt) REVERT: R 213 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7515 (mtm) REVERT: B 59 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.8321 (t80) REVERT: B 188 MET cc_start: 0.8413 (mmm) cc_final: 0.8065 (mmm) REVERT: B 234 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.6413 (m-80) REVERT: B 297 TRP cc_start: 0.7851 (m100) cc_final: 0.7427 (m100) outliers start: 28 outliers final: 21 residues processed: 168 average time/residue: 0.0711 time to fit residues: 16.8647 Evaluate side-chains 170 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 108 PHE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 3 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.178841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.143118 restraints weight = 8013.440| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.68 r_work: 0.3601 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7422 Z= 0.142 Angle : 0.599 8.617 10118 Z= 0.306 Chirality : 0.045 0.257 1179 Planarity : 0.005 0.103 1259 Dihedral : 4.384 29.240 1038 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.56 % Allowed : 29.20 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.28), residues: 937 helix: 1.45 (0.30), residues: 329 sheet: -0.38 (0.34), residues: 211 loop : -0.92 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG R 227 TYR 0.016 0.001 TYR A 339 PHE 0.014 0.001 PHE B 199 TRP 0.015 0.001 TRP A 281 HIS 0.004 0.001 HIS R 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 7418) covalent geometry : angle 0.59774 / 0.31 (10112) SS BOND : bond 0.00318 / 0.16 ( 3) SS BOND : angle 1.72070 / 0.88 ( 6) hydrogen bonds : bond 0.03520 / 2.45 ( 329) hydrogen bonds : angle 4.39959 / 3.19 ( 936) Misc. bond : bond 0.00059 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1660.07 seconds wall clock time: 29 minutes 6.87 seconds (1746.87 seconds total)