Starting phenix.real_space_refine on Wed Feb 4 11:13:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jh5_61472/02_2026/9jh5_61472.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jh5_61472/02_2026/9jh5_61472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jh5_61472/02_2026/9jh5_61472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jh5_61472/02_2026/9jh5_61472.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jh5_61472/02_2026/9jh5_61472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jh5_61472/02_2026/9jh5_61472.map" } resolution = 2.76 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= 0.037 sd= 0.849 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 970 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 6271 2.51 5 N 1676 2.21 5 O 1799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9808 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2077 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain breaks: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 422 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 51} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1783 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1878 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 3, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'16C': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.11, per 1000 atoms: 0.22 Number of scatterers: 9808 At special positions: 0 Unit cell: (83.64, 123, 127.92, 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 62 16.00 O 1799 8.00 N 1676 7.00 C 6271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 472.3 milliseconds 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2334 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 18 sheets defined 32.7% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'R' and resid 43 through 64 removed outlier: 3.754A pdb=" N LEU R 58 " --> pdb=" O LEU R 54 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER R 59 " --> pdb=" O GLY R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 100 Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 103 through 108 removed outlier: 3.841A pdb=" N GLY R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP R 108 " --> pdb=" O TRP R 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 103 through 108' Processing helix chain 'R' and resid 109 through 119 removed outlier: 4.316A pdb=" N ILE R 113 " --> pdb=" O LEU R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 142 removed outlier: 3.976A pdb=" N TYR R 123 " --> pdb=" O TYR R 119 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR R 127 " --> pdb=" O TYR R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 171 Processing helix chain 'R' and resid 198 through 210 removed outlier: 4.140A pdb=" N TYR R 203 " --> pdb=" O GLN R 199 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL R 208 " --> pdb=" O ILE R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 230 removed outlier: 3.756A pdb=" N PHE R 214 " --> pdb=" O CYS R 210 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE R 219 " --> pdb=" O PHE R 215 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL R 227 " --> pdb=" O LEU R 223 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS R 230 " --> pdb=" O ARG R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 270 removed outlier: 3.626A pdb=" N ARG R 243 " --> pdb=" O ARG R 239 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS R 244 " --> pdb=" O VAL R 240 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU R 261 " --> pdb=" O PHE R 257 " (cutoff:3.500A) Proline residue: R 262 - end of helix removed outlier: 4.086A pdb=" N LEU R 266 " --> pdb=" O PRO R 262 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS R 270 " --> pdb=" O LEU R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 307 removed outlier: 3.997A pdb=" N HIS R 284 " --> pdb=" O LYS R 280 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS R 299 " --> pdb=" O ALA R 295 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE R 300 " --> pdb=" O ALA R 296 " (cutoff:3.500A) Proline residue: R 302 - end of helix removed outlier: 3.555A pdb=" N TYR R 305 " --> pdb=" O ASN R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 316 removed outlier: 3.817A pdb=" N ARG R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU R 316 " --> pdb=" O PHE R 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.580A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 191 through 193 No H-bonds generated for 'chain 'S' and resid 191 through 193' Processing helix chain 'A' and resid 6 through 39 removed outlier: 3.519A pdb=" N GLN A 29 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.580A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.583A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.973A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.573A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.548A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 Processing sheet with id=AA1, first strand: chain 'S' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'S' and resid 45 through 51 removed outlier: 4.670A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 45 through 51 removed outlier: 4.670A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG S 98 " --> pdb=" O PHE S 110 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.548A pdb=" N THR S 213 " --> pdb=" O SER S 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 177 through 178 Processing sheet with id=AA7, first strand: chain 'S' and resid 189 through 190 Processing sheet with id=AA8, first strand: chain 'S' and resid 225 through 227 removed outlier: 3.847A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR S 243 " --> pdb=" O TYR S 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 210 through 213 removed outlier: 6.315A pdb=" N LEU A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE A 222 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.182A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.760A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.078A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.724A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.910A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.575A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.734A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.644A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 46 through 49 removed outlier: 6.331A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.37: 3448 1.37 - 1.60: 6468 1.60 - 1.84: 91 1.84 - 2.07: 3 2.07 - 2.31: 2 Bond restraints: 10012 Sorted by residual: bond pdb=" CD1 TYR S 94 " pdb=" CE1 TYR S 94 " ideal model delta sigma weight residual 1.382 2.306 -0.924 3.00e-02 1.11e+03 9.49e+02 bond pdb=" CD2 TYR S 94 " pdb=" CE2 TYR S 94 " ideal model delta sigma weight residual 1.382 2.242 -0.860 3.00e-02 1.11e+03 8.22e+02 bond pdb=" CD ARG S 38 " pdb=" NE ARG S 38 " ideal model delta sigma weight residual 1.458 1.844 -0.386 1.40e-02 5.10e+03 7.58e+02 bond pdb=" CE2 TYR S 94 " pdb=" CZ TYR S 94 " ideal model delta sigma weight residual 1.378 1.898 -0.520 2.40e-02 1.74e+03 4.69e+02 bond pdb=" CE1 TYR S 94 " pdb=" CZ TYR S 94 " ideal model delta sigma weight residual 1.378 1.894 -0.516 2.40e-02 1.74e+03 4.62e+02 ... (remaining 10007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.92: 13460 5.92 - 11.84: 93 11.84 - 17.76: 9 17.76 - 23.68: 1 23.68 - 29.60: 4 Bond angle restraints: 13567 Sorted by residual: angle pdb=" C ARG R 153 " pdb=" CA ARG R 153 " pdb=" CB ARG R 153 " ideal model delta sigma weight residual 109.16 80.53 28.63 1.29e+00 6.01e-01 4.93e+02 angle pdb=" CD ARG S 38 " pdb=" NE ARG S 38 " pdb=" CZ ARG S 38 " ideal model delta sigma weight residual 124.40 154.00 -29.60 1.40e+00 5.10e-01 4.47e+02 angle pdb=" N ARG R 153 " pdb=" CA ARG R 153 " pdb=" C ARG R 153 " ideal model delta sigma weight residual 114.75 140.78 -26.03 1.26e+00 6.30e-01 4.27e+02 angle pdb=" N LEU R 271 " pdb=" CA LEU R 271 " pdb=" C LEU R 271 " ideal model delta sigma weight residual 113.19 88.77 24.42 1.19e+00 7.06e-01 4.21e+02 angle pdb=" C ILE R 152 " pdb=" CA ILE R 152 " pdb=" CB ILE R 152 " ideal model delta sigma weight residual 111.70 132.47 -20.77 1.28e+00 6.10e-01 2.63e+02 ... (remaining 13562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.26: 5681 25.26 - 50.53: 305 50.53 - 75.79: 32 75.79 - 101.06: 10 101.06 - 126.32: 4 Dihedral angle restraints: 6032 sinusoidal: 2411 harmonic: 3621 Sorted by residual: dihedral pdb=" C ILE R 152 " pdb=" N ILE R 152 " pdb=" CA ILE R 152 " pdb=" CB ILE R 152 " ideal model delta harmonic sigma weight residual -122.00 -149.23 27.23 0 2.50e+00 1.60e-01 1.19e+02 dihedral pdb=" C TRP R 274 " pdb=" N TRP R 274 " pdb=" CA TRP R 274 " pdb=" CB TRP R 274 " ideal model delta harmonic sigma weight residual -122.60 -146.85 24.25 0 2.50e+00 1.60e-01 9.41e+01 dihedral pdb=" N TRP R 274 " pdb=" C TRP R 274 " pdb=" CA TRP R 274 " pdb=" CB TRP R 274 " ideal model delta harmonic sigma weight residual 122.80 146.65 -23.85 0 2.50e+00 1.60e-01 9.10e+01 ... (remaining 6029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 1521 0.231 - 0.461: 18 0.461 - 0.692: 6 0.692 - 0.922: 2 0.922 - 1.153: 1 Chirality restraints: 1548 Sorted by residual: chirality pdb=" CA TRP R 274 " pdb=" N TRP R 274 " pdb=" C TRP R 274 " pdb=" CB TRP R 274 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.32e+01 chirality pdb=" CA ILE R 152 " pdb=" N ILE R 152 " pdb=" C ILE R 152 " pdb=" CB ILE R 152 " both_signs ideal model delta sigma weight residual False 2.43 1.59 0.84 2.00e-01 2.50e+01 1.78e+01 chirality pdb=" CA PRO R 262 " pdb=" N PRO R 262 " pdb=" C PRO R 262 " pdb=" CB PRO R 262 " both_signs ideal model delta sigma weight residual False 2.72 1.95 0.76 2.00e-01 2.50e+01 1.46e+01 ... (remaining 1545 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 16C R 401 " -0.024 2.00e-02 2.50e+03 9.22e-02 1.06e+02 pdb=" C2 16C R 401 " 0.111 2.00e-02 2.50e+03 pdb=" C20 16C R 401 " 0.080 2.00e-02 2.50e+03 pdb=" N2 16C R 401 " -0.152 2.00e-02 2.50e+03 pdb=" O19 16C R 401 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 111 " 0.038 2.00e-02 2.50e+03 5.50e-02 7.57e+01 pdb=" CG TRP S 111 " -0.136 2.00e-02 2.50e+03 pdb=" CD1 TRP S 111 " 0.097 2.00e-02 2.50e+03 pdb=" CD2 TRP S 111 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP S 111 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TRP S 111 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP S 111 " 0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 111 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 111 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP S 111 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 261 " 0.131 5.00e-02 4.00e+02 1.98e-01 6.27e+01 pdb=" N PRO R 262 " -0.342 5.00e-02 4.00e+02 pdb=" CA PRO R 262 " 0.106 5.00e-02 4.00e+02 pdb=" CD PRO R 262 " 0.105 5.00e-02 4.00e+02 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 10 1.81 - 2.58: 192 2.58 - 3.36: 13068 3.36 - 4.13: 24779 4.13 - 4.90: 45825 Nonbonded interactions: 83874 Sorted by model distance: nonbonded pdb=" CA HIS R 284 " pdb=" CD2 LEU R 287 " model vdw 1.038 3.890 nonbonded pdb=" O VAL R 269 " pdb=" CG2 THR R 272 " model vdw 1.156 3.460 nonbonded pdb=" O ALA R 286 " pdb=" CG1 ILE R 289 " model vdw 1.176 3.440 nonbonded pdb=" O HIS R 284 " pdb=" CG LEU R 287 " model vdw 1.181 3.470 nonbonded pdb=" CB HIS R 284 " pdb=" CD2 LEU R 287 " model vdw 1.469 3.860 ... (remaining 83869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 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 : 0.024 0.924 10021 Z= 1.623 Angle : 1.384 29.601 13569 Z= 0.814 Chirality : 0.086 1.153 1548 Planarity : 0.009 0.198 1698 Dihedral : 15.928 126.324 3695 Min Nonbonded Distance : 1.038 Molprobity Statistics. All-atom Clashscore : 35.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.65 % Favored : 87.10 % Rotamer: Outliers : 1.82 % Allowed : 0.86 % Favored : 97.32 % Cbeta Deviations : 0.86 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.17 % 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: -2.92 (0.22), residues: 1225 helix: -0.52 (0.26), residues: 350 sheet: -1.52 (0.31), residues: 284 loop : -3.12 (0.22), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 118 TYR 0.059 0.004 TYR R 123 PHE 0.031 0.003 PHE S 68 TRP 0.136 0.005 TRP S 111 HIS 0.027 0.003 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.01985 (10012) covalent geometry : angle 1.38421 (13567) SS BOND : bond 0.00186 ( 1) SS BOND : angle 1.98775 ( 2) hydrogen bonds : bond 0.21071 ( 389) hydrogen bonds : angle 8.77936 ( 1092) Misc. bond : bond 0.47939 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 HIS cc_start: 0.4617 (OUTLIER) cc_final: 0.4234 (p90) REVERT: S 140 MET cc_start: 0.6937 (mmm) cc_final: 0.6359 (mmp) outliers start: 19 outliers final: 8 residues processed: 199 average time/residue: 0.4703 time to fit residues: 100.2937 Evaluate side-chains 139 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 140 MET Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 262 PRO Chi-restraints excluded: chain R residue 270 HIS Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain A residue 379 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 35 ASN R 56 ASN ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 HIS ** R 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 311 ASN ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 232 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 32 GLN B 75 GLN B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.099365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.092337 restraints weight = 31162.418| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.63 r_work: 0.3697 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10021 Z= 0.249 Angle : 0.918 11.413 13569 Z= 0.469 Chirality : 0.053 0.223 1548 Planarity : 0.007 0.076 1698 Dihedral : 10.438 83.704 1545 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.45 % Favored : 89.47 % Rotamer: Outliers : 4.60 % Allowed : 14.86 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.17 % 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: -2.43 (0.22), residues: 1225 helix: 0.01 (0.26), residues: 356 sheet: -1.23 (0.30), residues: 293 loop : -2.94 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG S 38 TYR 0.025 0.003 TYR S 94 PHE 0.023 0.003 PHE R 307 TRP 0.057 0.003 TRP R 274 HIS 0.015 0.003 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00578 (10012) covalent geometry : angle 0.91743 (13567) SS BOND : bond 0.00081 ( 1) SS BOND : angle 1.80752 ( 2) hydrogen bonds : bond 0.05681 ( 389) hydrogen bonds : angle 6.30595 ( 1092) Misc. bond : bond 0.00286 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 43 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6707 (mt) REVERT: R 116 TYR cc_start: 0.5787 (t80) cc_final: 0.5247 (t80) REVERT: C 22 GLU cc_start: 0.7699 (mp0) cc_final: 0.7397 (mt-10) REVERT: C 36 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8157 (t70) REVERT: S 160 ARG cc_start: 0.7293 (mmm-85) cc_final: 0.7067 (mmm-85) REVERT: A 14 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6721 (mt-10) REVERT: B 214 ARG cc_start: 0.6091 (OUTLIER) cc_final: 0.4889 (mmp-170) REVERT: B 228 ASP cc_start: 0.7852 (p0) cc_final: 0.7595 (p0) REVERT: N 34 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7277 (mtp) outliers start: 48 outliers final: 12 residues processed: 167 average time/residue: 0.4557 time to fit residues: 82.1961 Evaluate side-chains 141 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 255 ILE Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 212 PHE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 34 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 43 optimal weight: 0.7980 chunk 105 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 HIS R 297 ASN C 18 GLN S 183 GLN S 232 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 385 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.102995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.095769 restraints weight = 30699.279| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.68 r_work: 0.3765 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10021 Z= 0.137 Angle : 0.711 9.098 13569 Z= 0.363 Chirality : 0.046 0.174 1548 Planarity : 0.005 0.063 1698 Dihedral : 8.475 57.690 1529 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.65 % Favored : 91.27 % Rotamer: Outliers : 4.12 % Allowed : 18.89 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.23), residues: 1225 helix: 0.54 (0.26), residues: 362 sheet: -1.15 (0.29), residues: 303 loop : -2.71 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 38 TYR 0.058 0.002 TYR S 94 PHE 0.016 0.002 PHE S 177 TRP 0.040 0.002 TRP R 274 HIS 0.007 0.001 HIS R 284 Details of bonding type rmsd covalent geometry : bond 0.00297 (10012) covalent geometry : angle 0.71101 (13567) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.89014 ( 2) hydrogen bonds : bond 0.04166 ( 389) hydrogen bonds : angle 5.79629 ( 1092) Misc. bond : bond 0.00751 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5663 (t80) cc_final: 0.5109 (t80) REVERT: C 18 GLN cc_start: 0.7857 (tp40) cc_final: 0.5610 (mm110) REVERT: C 22 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6953 (mt-10) REVERT: C 36 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8132 (t0) REVERT: S 140 MET cc_start: 0.6801 (mmm) cc_final: 0.6362 (mmp) REVERT: S 160 ARG cc_start: 0.7398 (mmm-85) cc_final: 0.7155 (mmm-85) REVERT: B 45 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8204 (mtp) REVERT: B 85 TYR cc_start: 0.7439 (m-80) cc_final: 0.7201 (m-80) REVERT: B 214 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.4790 (mmp-170) REVERT: B 228 ASP cc_start: 0.7626 (p0) cc_final: 0.7184 (p0) REVERT: B 284 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6474 (mp) REVERT: N 73 ASP cc_start: 0.7082 (t0) cc_final: 0.6855 (t0) outliers start: 43 outliers final: 12 residues processed: 161 average time/residue: 0.4846 time to fit residues: 84.1204 Evaluate side-chains 143 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 212 PHE Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 55 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 75 optimal weight: 0.2980 chunk 86 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 56 ASN ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.101552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.094275 restraints weight = 31149.951| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.70 r_work: 0.3731 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10021 Z= 0.158 Angle : 0.736 11.759 13569 Z= 0.375 Chirality : 0.047 0.229 1548 Planarity : 0.006 0.084 1698 Dihedral : 8.248 57.069 1529 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.39 % Favored : 90.53 % Rotamer: Outliers : 5.75 % Allowed : 20.52 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.23), residues: 1225 helix: 0.82 (0.27), residues: 362 sheet: -0.99 (0.30), residues: 300 loop : -2.68 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 94 TYR 0.030 0.002 TYR S 94 PHE 0.016 0.002 PHE S 239 TRP 0.028 0.002 TRP R 274 HIS 0.018 0.002 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00363 (10012) covalent geometry : angle 0.73618 (13567) SS BOND : bond 0.00084 ( 1) SS BOND : angle 1.03780 ( 2) hydrogen bonds : bond 0.04298 ( 389) hydrogen bonds : angle 5.70740 ( 1092) Misc. bond : bond 0.00539 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 133 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5730 (t80) cc_final: 0.5242 (t80) REVERT: R 274 TRP cc_start: 0.4961 (p90) cc_final: 0.4748 (p90) REVERT: R 291 LEU cc_start: 0.5202 (pp) cc_final: 0.4958 (tm) REVERT: C 18 GLN cc_start: 0.7703 (tp40) cc_final: 0.5733 (mm110) REVERT: C 22 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6596 (mt-10) REVERT: C 36 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8077 (t70) REVERT: S 140 MET cc_start: 0.6857 (mmm) cc_final: 0.6410 (mmp) REVERT: S 160 ARG cc_start: 0.7467 (mmm-85) cc_final: 0.7231 (mmm-85) REVERT: S 184 SER cc_start: 0.6952 (OUTLIER) cc_final: 0.6752 (m) REVERT: A 357 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6677 (m-70) REVERT: B 85 TYR cc_start: 0.7518 (m-80) cc_final: 0.7279 (m-80) REVERT: B 214 ARG cc_start: 0.5936 (OUTLIER) cc_final: 0.4813 (mmp-170) REVERT: B 228 ASP cc_start: 0.7640 (p0) cc_final: 0.7162 (p0) REVERT: B 284 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6507 (mp) REVERT: N 5 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.6676 (mt0) outliers start: 60 outliers final: 19 residues processed: 174 average time/residue: 0.4274 time to fit residues: 81.0009 Evaluate side-chains 154 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 98 optimal weight: 0.0370 chunk 84 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 56 ASN R 121 ASN R 148 HIS S 39 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN N 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.102482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.095189 restraints weight = 30568.517| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.69 r_work: 0.3751 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10021 Z= 0.138 Angle : 0.715 12.662 13569 Z= 0.359 Chirality : 0.045 0.197 1548 Planarity : 0.005 0.057 1698 Dihedral : 8.080 56.314 1529 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.65 % Favored : 91.27 % Rotamer: Outliers : 5.85 % Allowed : 20.90 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.24), residues: 1225 helix: 1.08 (0.27), residues: 364 sheet: -0.99 (0.29), residues: 309 loop : -2.62 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 94 TYR 0.035 0.002 TYR S 94 PHE 0.019 0.002 PHE S 177 TRP 0.024 0.002 TRP R 274 HIS 0.016 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00306 (10012) covalent geometry : angle 0.71543 (13567) SS BOND : bond 0.00156 ( 1) SS BOND : angle 0.73591 ( 2) hydrogen bonds : bond 0.03925 ( 389) hydrogen bonds : angle 5.59506 ( 1092) Misc. bond : bond 0.00665 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 142 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5820 (t80) cc_final: 0.5367 (t80) REVERT: R 291 LEU cc_start: 0.5093 (pp) cc_final: 0.4814 (tm) REVERT: C 18 GLN cc_start: 0.7651 (tp40) cc_final: 0.5823 (mm110) REVERT: C 22 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6532 (mt-10) REVERT: S 95 TYR cc_start: 0.4841 (m-10) cc_final: 0.4580 (m-10) REVERT: S 140 MET cc_start: 0.6796 (mmm) cc_final: 0.6489 (mmp) REVERT: S 160 ARG cc_start: 0.7612 (mmm-85) cc_final: 0.7305 (mmm-85) REVERT: S 235 TYR cc_start: 0.6513 (OUTLIER) cc_final: 0.5812 (m-80) REVERT: A 14 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6294 (mt-10) REVERT: A 357 HIS cc_start: 0.6974 (OUTLIER) cc_final: 0.6448 (m-70) REVERT: B 45 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8202 (mtp) REVERT: B 85 TYR cc_start: 0.7514 (m-80) cc_final: 0.7262 (m-80) REVERT: B 214 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.4785 (mmp-170) REVERT: B 284 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.6471 (mp) outliers start: 61 outliers final: 24 residues processed: 179 average time/residue: 0.4122 time to fit residues: 80.5307 Evaluate side-chains 160 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 306 TYR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 103 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 112 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 56 ASN R 148 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.102922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.095709 restraints weight = 30566.988| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.69 r_work: 0.3759 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10021 Z= 0.132 Angle : 0.686 11.647 13569 Z= 0.349 Chirality : 0.045 0.229 1548 Planarity : 0.005 0.112 1698 Dihedral : 7.997 59.753 1529 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.57 % Favored : 91.35 % Rotamer: Outliers : 5.18 % Allowed : 22.72 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.24), residues: 1225 helix: 1.19 (0.27), residues: 364 sheet: -0.78 (0.29), residues: 299 loop : -2.55 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 38 TYR 0.083 0.002 TYR S 94 PHE 0.017 0.002 PHE S 177 TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00298 (10012) covalent geometry : angle 0.68573 (13567) SS BOND : bond 0.00223 ( 1) SS BOND : angle 0.67040 ( 2) hydrogen bonds : bond 0.03872 ( 389) hydrogen bonds : angle 5.42011 ( 1092) Misc. bond : bond 0.00559 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 139 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5830 (t80) cc_final: 0.5411 (t80) REVERT: R 167 MET cc_start: 0.5320 (mmm) cc_final: 0.3558 (mmm) REVERT: C 18 GLN cc_start: 0.7610 (tp40) cc_final: 0.5947 (mp10) REVERT: C 22 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: S 140 MET cc_start: 0.6832 (mmm) cc_final: 0.6506 (mmp) REVERT: S 235 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.5854 (m-80) REVERT: A 14 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6173 (mt-10) REVERT: A 357 HIS cc_start: 0.6930 (OUTLIER) cc_final: 0.6397 (m-70) REVERT: B 45 MET cc_start: 0.8464 (mtp) cc_final: 0.8174 (mtp) REVERT: B 85 TYR cc_start: 0.7533 (m-10) cc_final: 0.7315 (m-80) REVERT: B 214 ARG cc_start: 0.5927 (OUTLIER) cc_final: 0.4809 (mmp-170) REVERT: N 5 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.6632 (mt0) outliers start: 54 outliers final: 24 residues processed: 174 average time/residue: 0.3916 time to fit residues: 74.2996 Evaluate side-chains 161 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 84 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 35 ASN R 56 ASN R 103 ASN R 148 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 259 GLN N 5 GLN N 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.101490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.094355 restraints weight = 30459.851| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.67 r_work: 0.3732 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10021 Z= 0.153 Angle : 0.717 11.926 13569 Z= 0.363 Chirality : 0.046 0.236 1548 Planarity : 0.005 0.054 1698 Dihedral : 8.054 57.863 1529 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.31 % Favored : 90.61 % Rotamer: Outliers : 5.47 % Allowed : 23.49 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.24), residues: 1225 helix: 1.16 (0.27), residues: 364 sheet: -0.78 (0.29), residues: 303 loop : -2.54 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG S 38 TYR 0.022 0.002 TYR S 94 PHE 0.017 0.002 PHE S 177 TRP 0.014 0.002 TRP B 211 HIS 0.011 0.002 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00354 (10012) covalent geometry : angle 0.71663 (13567) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.99348 ( 2) hydrogen bonds : bond 0.04085 ( 389) hydrogen bonds : angle 5.42400 ( 1092) Misc. bond : bond 0.00490 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 133 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5773 (t80) cc_final: 0.5282 (t80) REVERT: R 247 THR cc_start: 0.6651 (p) cc_final: 0.6294 (p) REVERT: C 18 GLN cc_start: 0.7682 (tp40) cc_final: 0.5898 (mm110) REVERT: C 22 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6736 (mt-10) REVERT: S 140 MET cc_start: 0.6937 (mmm) cc_final: 0.6627 (mmp) REVERT: S 184 SER cc_start: 0.6620 (t) cc_final: 0.6345 (m) REVERT: S 235 TYR cc_start: 0.6623 (OUTLIER) cc_final: 0.5892 (m-80) REVERT: A 14 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6155 (mt-10) REVERT: A 215 ASP cc_start: 0.6793 (m-30) cc_final: 0.6580 (m-30) REVERT: A 231 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.6792 (ptt180) REVERT: A 357 HIS cc_start: 0.6965 (OUTLIER) cc_final: 0.6478 (m-70) REVERT: B 45 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8215 (mtp) REVERT: B 85 TYR cc_start: 0.7509 (m-10) cc_final: 0.7271 (m-80) REVERT: B 214 ARG cc_start: 0.5950 (OUTLIER) cc_final: 0.4846 (mmp-170) REVERT: B 284 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6446 (mp) REVERT: N 34 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.6842 (mtp) outliers start: 57 outliers final: 26 residues processed: 170 average time/residue: 0.3955 time to fit residues: 72.9677 Evaluate side-chains 163 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 63 optimal weight: 0.0870 chunk 82 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 0.0030 chunk 41 optimal weight: 6.9990 overall best weight: 1.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 56 ASN R 148 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN N 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.100958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.093851 restraints weight = 30504.025| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.66 r_work: 0.3720 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10021 Z= 0.161 Angle : 0.744 11.023 13569 Z= 0.379 Chirality : 0.046 0.251 1548 Planarity : 0.005 0.059 1698 Dihedral : 8.175 59.409 1529 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.63 % Favored : 90.29 % Rotamer: Outliers : 6.33 % Allowed : 23.68 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.24), residues: 1225 helix: 1.09 (0.27), residues: 364 sheet: -0.74 (0.30), residues: 295 loop : -2.46 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG R 94 TYR 0.045 0.002 TYR S 94 PHE 0.017 0.002 PHE S 177 TRP 0.015 0.002 TRP B 211 HIS 0.007 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00369 (10012) covalent geometry : angle 0.74449 (13567) SS BOND : bond 0.00226 ( 1) SS BOND : angle 0.74099 ( 2) hydrogen bonds : bond 0.04135 ( 389) hydrogen bonds : angle 5.49539 ( 1092) Misc. bond : bond 0.00589 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 131 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5825 (t80) cc_final: 0.5269 (t80) REVERT: R 119 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.5897 (m-10) REVERT: R 167 MET cc_start: 0.4555 (mmp) cc_final: 0.3088 (mmm) REVERT: R 247 THR cc_start: 0.6597 (p) cc_final: 0.6266 (p) REVERT: R 311 ASN cc_start: 0.7636 (t0) cc_final: 0.7350 (t160) REVERT: C 18 GLN cc_start: 0.7623 (tp40) cc_final: 0.6025 (mm110) REVERT: C 22 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6771 (mt-10) REVERT: S 140 MET cc_start: 0.7007 (mmm) cc_final: 0.6652 (mmp) REVERT: S 235 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.5892 (m-80) REVERT: A 60 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7571 (mtm) REVERT: A 215 ASP cc_start: 0.6783 (m-30) cc_final: 0.6558 (m-30) REVERT: A 231 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6835 (ptt180) REVERT: A 357 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6566 (m-70) REVERT: B 45 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8201 (mtp) REVERT: B 214 ARG cc_start: 0.6018 (OUTLIER) cc_final: 0.4913 (mmp-170) REVERT: B 284 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6411 (mp) REVERT: N 5 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6589 (mt0) REVERT: N 34 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.6955 (mtp) outliers start: 66 outliers final: 32 residues processed: 172 average time/residue: 0.4043 time to fit residues: 76.2171 Evaluate side-chains 166 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 119 TYR Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 0.0040 chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 148 HIS R 311 ASN ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.102730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.095605 restraints weight = 30384.009| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.65 r_work: 0.3753 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10021 Z= 0.131 Angle : 0.700 11.359 13569 Z= 0.356 Chirality : 0.045 0.261 1548 Planarity : 0.005 0.062 1698 Dihedral : 7.981 58.468 1529 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.24 % Favored : 91.67 % Rotamer: Outliers : 4.79 % Allowed : 25.89 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.24), residues: 1225 helix: 1.17 (0.28), residues: 354 sheet: -0.70 (0.29), residues: 298 loop : -2.37 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 94 TYR 0.036 0.002 TYR S 94 PHE 0.017 0.002 PHE R 300 TRP 0.016 0.002 TRP R 274 HIS 0.006 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00300 (10012) covalent geometry : angle 0.69943 (13567) SS BOND : bond 0.00010 ( 1) SS BOND : angle 1.25818 ( 2) hydrogen bonds : bond 0.03797 ( 389) hydrogen bonds : angle 5.41869 ( 1092) Misc. bond : bond 0.00497 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 135 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5658 (t80) cc_final: 0.5188 (t80) REVERT: R 119 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.5604 (m-10) REVERT: R 167 MET cc_start: 0.4543 (mmp) cc_final: 0.4223 (mmp) REVERT: R 207 VAL cc_start: 0.6334 (p) cc_final: 0.6066 (t) REVERT: C 18 GLN cc_start: 0.7592 (tp40) cc_final: 0.6538 (mp10) REVERT: S 140 MET cc_start: 0.7068 (mmm) cc_final: 0.6733 (mmp) REVERT: S 235 TYR cc_start: 0.6557 (OUTLIER) cc_final: 0.5867 (m-80) REVERT: A 14 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6211 (mt-10) REVERT: A 60 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7548 (mtm) REVERT: A 215 ASP cc_start: 0.6797 (m-30) cc_final: 0.6585 (m-30) REVERT: A 357 HIS cc_start: 0.6926 (OUTLIER) cc_final: 0.6374 (m-70) REVERT: B 45 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8178 (mtp) REVERT: B 214 ARG cc_start: 0.5988 (OUTLIER) cc_final: 0.4852 (mmp-170) outliers start: 50 outliers final: 26 residues processed: 165 average time/residue: 0.4003 time to fit residues: 72.1208 Evaluate side-chains 152 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 119 TYR Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 92 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 148 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.102438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.095298 restraints weight = 30192.006| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.66 r_work: 0.3750 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10021 Z= 0.139 Angle : 0.720 11.986 13569 Z= 0.367 Chirality : 0.046 0.268 1548 Planarity : 0.005 0.060 1698 Dihedral : 7.939 58.479 1529 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.33 % Favored : 91.59 % Rotamer: Outliers : 4.03 % Allowed : 27.23 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.24), residues: 1225 helix: 1.16 (0.27), residues: 358 sheet: -0.74 (0.29), residues: 303 loop : -2.37 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 94 TYR 0.092 0.002 TYR S 94 PHE 0.017 0.002 PHE S 177 TRP 0.020 0.002 TRP R 274 HIS 0.007 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00318 (10012) covalent geometry : angle 0.72027 (13567) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.58460 ( 2) hydrogen bonds : bond 0.03873 ( 389) hydrogen bonds : angle 5.39226 ( 1092) Misc. bond : bond 0.00560 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5727 (t80) cc_final: 0.5240 (t80) REVERT: R 119 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.5491 (m-10) REVERT: R 167 MET cc_start: 0.4573 (mmp) cc_final: 0.4260 (mmp) REVERT: R 207 VAL cc_start: 0.6395 (p) cc_final: 0.6119 (t) REVERT: C 18 GLN cc_start: 0.7359 (tp40) cc_final: 0.6499 (mp10) REVERT: C 22 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7008 (mm-30) REVERT: S 140 MET cc_start: 0.7091 (mmm) cc_final: 0.6719 (mmp) REVERT: S 184 SER cc_start: 0.6458 (t) cc_final: 0.6243 (m) REVERT: S 235 TYR cc_start: 0.6539 (OUTLIER) cc_final: 0.5839 (m-80) REVERT: A 14 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6249 (mt-10) REVERT: A 215 ASP cc_start: 0.6791 (m-30) cc_final: 0.6548 (m-30) REVERT: A 231 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6795 (ptt180) REVERT: A 357 HIS cc_start: 0.6922 (OUTLIER) cc_final: 0.6367 (m-70) REVERT: B 45 MET cc_start: 0.8462 (mtp) cc_final: 0.8182 (mtp) REVERT: B 214 ARG cc_start: 0.5938 (OUTLIER) cc_final: 0.4803 (mmp-170) REVERT: B 228 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7137 (p0) REVERT: B 284 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6457 (mp) outliers start: 42 outliers final: 26 residues processed: 152 average time/residue: 0.3882 time to fit residues: 64.6112 Evaluate side-chains 154 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 119 TYR Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 92 optimal weight: 7.9990 chunk 62 optimal weight: 0.0670 chunk 96 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 148 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** 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 = 0.3958 r_free = 0.3958 target = 0.103251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.096071 restraints weight = 30409.413| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.67 r_work: 0.3765 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10021 Z= 0.137 Angle : 0.719 13.777 13569 Z= 0.366 Chirality : 0.045 0.277 1548 Planarity : 0.005 0.054 1698 Dihedral : 7.890 58.113 1529 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.08 % Favored : 91.84 % Rotamer: Outliers : 3.74 % Allowed : 27.52 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.24), residues: 1225 helix: 1.18 (0.27), residues: 357 sheet: -0.75 (0.29), residues: 305 loop : -2.35 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 94 TYR 0.108 0.002 TYR S 94 PHE 0.016 0.002 PHE R 300 TRP 0.017 0.002 TRP R 274 HIS 0.008 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00307 (10012) covalent geometry : angle 0.71882 (13567) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.60696 ( 2) hydrogen bonds : bond 0.03832 ( 389) hydrogen bonds : angle 5.40250 ( 1092) Misc. bond : bond 0.00648 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2962.18 seconds wall clock time: 51 minutes 17.92 seconds (3077.92 seconds total)