Starting phenix.real_space_refine on Mon Jul 28 13:44:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jh5_61472/07_2025/9jh5_61472.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jh5_61472/07_2025/9jh5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jh5_61472/07_2025/9jh5_61472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jh5_61472/07_2025/9jh5_61472.map" model { file = "/net/cci-nas-00/data/ceres_data/9jh5_61472/07_2025/9jh5_61472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jh5_61472/07_2025/9jh5_61472.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.037 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'PHE:plan': 1, 'GLU: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, 'GLU:plan': 5, 'ASP:plan': 3, 'HIS:plan': 1} 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: 7.07, per 1000 atoms: 0.72 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: 2.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.92 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: 2.95 Time building geometry restraints manager: 3.25 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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.130 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:49.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.910 ------------------------------------------------------------------------------- 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 : 35.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.136 0.005 TRP S 111 HIS 0.027 0.003 HIS A 357 PHE 0.031 0.003 PHE S 68 TYR 0.059 0.004 TYR R 123 ARG 0.013 0.001 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.21071 ( 389) hydrogen bonds : angle 8.77936 ( 1092) SS BOND : bond 0.00186 ( 1) SS BOND : angle 1.98775 ( 2) covalent geometry : bond 0.01985 (10012) covalent geometry : angle 1.38421 (13567) 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 : 1.700 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: 1.2469 time to fit residues: 266.1574 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 : 1.018 ------------------------------------------------------------------------------- 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 102 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.104443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.097136 restraints weight = 31033.832| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.67 r_work: 0.3793 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10021 Z= 0.157 Angle : 0.780 12.074 13569 Z= 0.397 Chirality : 0.048 0.197 1548 Planarity : 0.006 0.071 1698 Dihedral : 9.809 76.611 1545 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.65 % Favored : 91.27 % Rotamer: Outliers : 3.36 % Allowed : 13.14 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.23), residues: 1225 helix: 0.37 (0.27), residues: 354 sheet: -1.20 (0.30), residues: 291 loop : -2.84 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP R 274 HIS 0.009 0.002 HIS A 357 PHE 0.021 0.002 PHE R 307 TYR 0.023 0.002 TYR S 94 ARG 0.014 0.001 ARG S 38 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 389) hydrogen bonds : angle 6.19928 ( 1092) SS BOND : bond 0.00082 ( 1) SS BOND : angle 1.35543 ( 2) covalent geometry : bond 0.00346 (10012) covalent geometry : angle 0.78015 (13567) Misc. bond : bond 0.00348 ( 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 178 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5694 (t80) cc_final: 0.5260 (t80) REVERT: R 215 PHE cc_start: 0.8101 (m-80) cc_final: 0.7888 (m-80) REVERT: C 22 GLU cc_start: 0.7388 (mp0) cc_final: 0.7111 (mt-10) REVERT: S 5 VAL cc_start: 0.7174 (m) cc_final: 0.6822 (p) REVERT: S 140 MET cc_start: 0.7098 (mmm) cc_final: 0.6689 (mmt) REVERT: S 201 ASP cc_start: 0.5969 (t0) cc_final: 0.5663 (t70) REVERT: B 214 ARG cc_start: 0.5801 (OUTLIER) cc_final: 0.4686 (mmp-170) outliers start: 35 outliers final: 8 residues processed: 158 average time/residue: 1.3714 time to fit residues: 233.2024 Evaluate side-chains 136 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 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 S residue 212 PHE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 113 optimal weight: 0.0070 chunk 30 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 37 optimal weight: 0.0010 chunk 22 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 overall best weight: 0.4604 ------------------------------------------------------------------------------- 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 R 311 ASN C 18 GLN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN N 1 GLN N 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.105796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.098302 restraints weight = 30995.680| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.71 r_work: 0.3813 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3052 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= 0.126 Angle : 0.676 9.416 13569 Z= 0.346 Chirality : 0.045 0.213 1548 Planarity : 0.005 0.061 1698 Dihedral : 8.325 58.292 1529 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.08 % Favored : 91.84 % Rotamer: Outliers : 3.55 % Allowed : 17.35 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.23), residues: 1225 helix: 0.81 (0.27), residues: 360 sheet: -1.24 (0.29), residues: 302 loop : -2.54 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 274 HIS 0.006 0.001 HIS R 284 PHE 0.013 0.001 PHE S 239 TYR 0.042 0.002 TYR S 94 ARG 0.011 0.001 ARG S 38 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 389) hydrogen bonds : angle 5.71989 ( 1092) SS BOND : bond 0.00047 ( 1) SS BOND : angle 0.86614 ( 2) covalent geometry : bond 0.00270 (10012) covalent geometry : angle 0.67580 (13567) Misc. bond : bond 0.00676 ( 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 184 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.787 Fit side-chains revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5640 (t80) cc_final: 0.5224 (t80) REVERT: C 18 GLN cc_start: 0.7698 (tp40) cc_final: 0.6006 (mm110) REVERT: C 36 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8127 (t70) REVERT: S 5 VAL cc_start: 0.7009 (m) cc_final: 0.6610 (p) REVERT: S 140 MET cc_start: 0.7134 (mmm) cc_final: 0.6749 (mmp) REVERT: S 160 ARG cc_start: 0.7428 (mmm-85) cc_final: 0.7141 (mmm-85) REVERT: S 201 ASP cc_start: 0.5917 (t0) cc_final: 0.5621 (t0) REVERT: A 14 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6222 (mt-10) REVERT: B 45 MET cc_start: 0.8476 (mtp) cc_final: 0.8163 (mtp) REVERT: B 85 TYR cc_start: 0.7544 (m-80) cc_final: 0.7343 (m-80) REVERT: N 73 ASP cc_start: 0.7080 (t0) cc_final: 0.6847 (t0) outliers start: 37 outliers final: 9 residues processed: 162 average time/residue: 1.3457 time to fit residues: 236.6126 Evaluate side-chains 139 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 ILE 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 30 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 35 ASN ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 HIS ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.100370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.093123 restraints weight = 30636.586| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.66 r_work: 0.3712 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10021 Z= 0.208 Angle : 0.818 16.365 13569 Z= 0.419 Chirality : 0.050 0.196 1548 Planarity : 0.006 0.076 1698 Dihedral : 8.633 56.752 1529 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.29 % Favored : 89.63 % Rotamer: Outliers : 5.27 % Allowed : 18.12 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.23), residues: 1225 helix: 0.78 (0.27), residues: 364 sheet: -1.12 (0.29), residues: 309 loop : -2.73 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP R 274 HIS 0.012 0.002 HIS A 357 PHE 0.023 0.003 PHE S 239 TYR 0.031 0.003 TYR S 94 ARG 0.015 0.001 ARG R 94 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 389) hydrogen bonds : angle 5.79800 ( 1092) SS BOND : bond 0.00181 ( 1) SS BOND : angle 1.65846 ( 2) covalent geometry : bond 0.00481 (10012) covalent geometry : angle 0.81803 (13567) Misc. bond : bond 0.00419 ( 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 186 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 131 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 43 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6732 (mt) REVERT: R 116 TYR cc_start: 0.5905 (t80) cc_final: 0.5384 (t80) REVERT: R 310 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6805 (tm-30) REVERT: R 311 ASN cc_start: 0.7572 (t0) cc_final: 0.7365 (t160) REVERT: C 18 GLN cc_start: 0.7520 (tp40) cc_final: 0.6353 (mm110) REVERT: C 36 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8143 (t70) REVERT: C 62 ARG cc_start: 0.5770 (OUTLIER) cc_final: 0.5077 (mtm-85) REVERT: S 5 VAL cc_start: 0.7381 (m) cc_final: 0.6976 (p) REVERT: S 140 MET cc_start: 0.7191 (mmm) cc_final: 0.6885 (mmp) REVERT: S 184 SER cc_start: 0.6713 (OUTLIER) cc_final: 0.6433 (m) REVERT: A 215 ASP cc_start: 0.6871 (m-30) cc_final: 0.6648 (m-30) REVERT: A 343 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7640 (tmmt) REVERT: B 85 TYR cc_start: 0.7746 (m-80) cc_final: 0.7517 (m-80) REVERT: B 214 ARG cc_start: 0.6047 (OUTLIER) cc_final: 0.4909 (mmp-170) REVERT: N 34 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7248 (mtp) outliers start: 55 outliers final: 18 residues processed: 167 average time/residue: 1.0923 time to fit residues: 198.7831 Evaluate side-chains 151 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 ILE 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 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 22 GLU 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 C residue 62 ARG Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 38 ASP 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 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 34 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 97 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 35 ASN R 121 ASN R 148 HIS ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 232 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN B 75 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.102180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.094829 restraints weight = 30229.102| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.66 r_work: 0.3745 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10021 Z= 0.145 Angle : 0.717 12.034 13569 Z= 0.363 Chirality : 0.046 0.177 1548 Planarity : 0.005 0.057 1698 Dihedral : 8.292 57.616 1529 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.90 % Favored : 91.02 % Rotamer: Outliers : 5.85 % Allowed : 20.04 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.23), residues: 1225 helix: 0.95 (0.27), residues: 364 sheet: -1.07 (0.29), residues: 305 loop : -2.64 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 274 HIS 0.017 0.002 HIS R 270 PHE 0.020 0.002 PHE S 239 TYR 0.027 0.002 TYR S 94 ARG 0.008 0.001 ARG R 94 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 389) hydrogen bonds : angle 5.56629 ( 1092) SS BOND : bond 0.00186 ( 1) SS BOND : angle 0.89196 ( 2) covalent geometry : bond 0.00327 (10012) covalent geometry : angle 0.71706 (13567) Misc. bond : bond 0.00624 ( 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 197 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 136 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5801 (t80) cc_final: 0.5372 (t80) REVERT: C 18 GLN cc_start: 0.7287 (tp40) cc_final: 0.6416 (mm110) REVERT: S 5 VAL cc_start: 0.7334 (m) cc_final: 0.6933 (p) REVERT: S 140 MET cc_start: 0.7226 (mmm) cc_final: 0.6883 (mmp) REVERT: S 184 SER cc_start: 0.6627 (OUTLIER) cc_final: 0.6351 (m) REVERT: S 235 TYR cc_start: 0.6554 (OUTLIER) cc_final: 0.5816 (m-80) REVERT: A 357 HIS cc_start: 0.7042 (OUTLIER) cc_final: 0.6638 (m-70) REVERT: B 85 TYR cc_start: 0.7546 (m-80) cc_final: 0.7329 (m-80) REVERT: B 214 ARG cc_start: 0.5999 (OUTLIER) cc_final: 0.4900 (mmp-170) REVERT: B 284 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6494 (mp) REVERT: N 73 ASP cc_start: 0.7014 (t0) cc_final: 0.6796 (t0) outliers start: 61 outliers final: 27 residues processed: 172 average time/residue: 0.9211 time to fit residues: 173.2533 Evaluate side-chains 160 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 58 LEU Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 157 ILE 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 R residue 290 THR 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 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 S residue 235 TYR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 120 ILE 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 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 73 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 35 ASN R 148 HIS R 297 ASN R 311 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.101362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.094154 restraints weight = 30417.586| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.65 r_work: 0.3732 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 10021 Z= 0.167 Angle : 0.767 18.502 13569 Z= 0.387 Chirality : 0.047 0.359 1548 Planarity : 0.005 0.086 1698 Dihedral : 8.132 59.655 1529 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.31 % Favored : 90.61 % Rotamer: Outliers : 6.04 % Allowed : 22.05 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.23), residues: 1225 helix: 0.92 (0.27), residues: 366 sheet: -0.91 (0.29), residues: 297 loop : -2.68 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 274 HIS 0.047 0.003 HIS R 270 PHE 0.018 0.002 PHE S 239 TYR 0.066 0.002 TYR S 94 ARG 0.031 0.001 ARG S 38 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 389) hydrogen bonds : angle 5.59100 ( 1092) SS BOND : bond 0.00206 ( 1) SS BOND : angle 1.00806 ( 2) covalent geometry : bond 0.00383 (10012) covalent geometry : angle 0.76745 (13567) Misc. bond : bond 0.00950 ( 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 197 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 134 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5822 (t80) cc_final: 0.5342 (t80) REVERT: R 167 MET cc_start: 0.5394 (mmm) cc_final: 0.3649 (mmm) REVERT: C 18 GLN cc_start: 0.7309 (tp40) cc_final: 0.6437 (mm110) REVERT: S 5 VAL cc_start: 0.7369 (m) cc_final: 0.6943 (p) REVERT: S 140 MET cc_start: 0.7270 (mmm) cc_final: 0.6975 (mmp) REVERT: S 184 SER cc_start: 0.6657 (OUTLIER) cc_final: 0.6384 (m) REVERT: S 235 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.5901 (m-80) REVERT: A 14 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6346 (mt-10) REVERT: A 343 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7742 (tmmt) REVERT: A 357 HIS cc_start: 0.7052 (OUTLIER) cc_final: 0.6568 (m-70) REVERT: B 214 ARG cc_start: 0.6068 (OUTLIER) cc_final: 0.4948 (mmp-170) REVERT: B 284 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6415 (mp) REVERT: N 34 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7054 (mtp) outliers start: 63 outliers final: 31 residues processed: 174 average time/residue: 0.9271 time to fit residues: 176.7473 Evaluate side-chains 163 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 150 THR Chi-restraints excluded: chain R residue 157 ILE 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 R residue 290 THR 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 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 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 343 LYS 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 120 ILE 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 284 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 93 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 78 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 148 HIS S 3 GLN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.096615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.089894 restraints weight = 30996.838| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.59 r_work: 0.3649 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 10021 Z= 0.280 Angle : 0.953 13.941 13569 Z= 0.484 Chirality : 0.054 0.298 1548 Planarity : 0.007 0.060 1698 Dihedral : 8.973 58.928 1529 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.86 % Favored : 89.06 % Rotamer: Outliers : 7.57 % Allowed : 21.86 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.23), residues: 1225 helix: 0.49 (0.27), residues: 365 sheet: -1.02 (0.28), residues: 320 loop : -2.88 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP R 274 HIS 0.050 0.004 HIS R 270 PHE 0.025 0.004 PHE S 203 TYR 0.065 0.004 TYR S 94 ARG 0.009 0.001 ARG R 94 Details of bonding type rmsd hydrogen bonds : bond 0.05358 ( 389) hydrogen bonds : angle 5.97769 ( 1092) SS BOND : bond 0.00277 ( 1) SS BOND : angle 2.81641 ( 2) covalent geometry : bond 0.00661 (10012) covalent geometry : angle 0.95264 (13567) Misc. bond : bond 0.00962 ( 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 210 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 131 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 56 ASN cc_start: 0.6141 (OUTLIER) cc_final: 0.5925 (m110) REVERT: R 119 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6573 (m-10) REVERT: R 222 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8256 (mp) REVERT: C 18 GLN cc_start: 0.7475 (tp40) cc_final: 0.5983 (mm110) REVERT: C 22 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6532 (mp0) REVERT: C 36 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8161 (t70) REVERT: S 5 VAL cc_start: 0.7571 (m) cc_final: 0.7194 (p) REVERT: S 83 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5175 (tpt) REVERT: S 157 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7008 (tp) REVERT: S 184 SER cc_start: 0.7079 (OUTLIER) cc_final: 0.6795 (m) REVERT: S 235 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.5903 (m-80) REVERT: A 14 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6362 (mt-10) REVERT: A 18 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8154 (tpp) REVERT: A 343 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7740 (tmmt) REVERT: A 357 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.7058 (m-70) REVERT: B 214 ARG cc_start: 0.6204 (OUTLIER) cc_final: 0.5149 (mmp-170) REVERT: B 284 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6482 (mp) REVERT: N 34 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7596 (mtp) REVERT: N 90 ASP cc_start: 0.7803 (p0) cc_final: 0.7469 (p0) outliers start: 79 outliers final: 33 residues processed: 184 average time/residue: 0.9598 time to fit residues: 192.9614 Evaluate side-chains 163 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 115 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 119 TYR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 216 THR Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 246 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 R residue 290 THR 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 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 C residue 54 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 184 SER 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 343 LYS Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 38 ASP 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 B residue 243 THR 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 17 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 93 VAL 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 25 optimal weight: 0.1980 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 148 HIS S 3 GLN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.098069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.091240 restraints weight = 30889.711| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.62 r_work: 0.3670 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 10021 Z= 0.202 Angle : 0.833 13.848 13569 Z= 0.425 Chirality : 0.050 0.262 1548 Planarity : 0.006 0.058 1698 Dihedral : 8.892 59.451 1529 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.39 % Favored : 90.53 % Rotamer: Outliers : 6.04 % Allowed : 24.93 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.23), residues: 1225 helix: 0.65 (0.27), residues: 365 sheet: -1.06 (0.28), residues: 326 loop : -2.80 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 274 HIS 0.030 0.002 HIS R 270 PHE 0.025 0.003 PHE R 300 TYR 0.056 0.003 TYR S 94 ARG 0.020 0.001 ARG R 94 Details of bonding type rmsd hydrogen bonds : bond 0.04715 ( 389) hydrogen bonds : angle 5.76832 ( 1092) SS BOND : bond 0.00101 ( 1) SS BOND : angle 2.12362 ( 2) covalent geometry : bond 0.00475 (10012) covalent geometry : angle 0.83232 (13567) Misc. bond : bond 0.00803 ( 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 182 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 119 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5947 (t80) cc_final: 0.5592 (t80) REVERT: R 119 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6421 (m-10) REVERT: R 167 MET cc_start: 0.5106 (mmm) cc_final: 0.3662 (mmm) REVERT: R 222 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8268 (mp) REVERT: C 18 GLN cc_start: 0.7342 (tp40) cc_final: 0.5995 (mm110) REVERT: C 22 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: S 5 VAL cc_start: 0.7591 (m) cc_final: 0.7242 (p) REVERT: S 39 GLN cc_start: 0.5660 (pt0) cc_final: 0.5460 (pt0) REVERT: S 157 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.6938 (tp) REVERT: S 184 SER cc_start: 0.6901 (OUTLIER) cc_final: 0.6593 (m) REVERT: S 235 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.5846 (m-80) REVERT: A 14 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6260 (mt-10) REVERT: A 18 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8125 (tpp) REVERT: A 231 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6560 (ptt180) REVERT: A 272 ASP cc_start: 0.8419 (m-30) cc_final: 0.8102 (t0) REVERT: A 343 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7762 (tmmt) REVERT: A 357 HIS cc_start: 0.7178 (OUTLIER) cc_final: 0.6940 (m-70) REVERT: B 214 ARG cc_start: 0.6077 (OUTLIER) cc_final: 0.4950 (mmp-170) REVERT: B 284 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6402 (mp) REVERT: N 34 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7500 (mtp) REVERT: N 90 ASP cc_start: 0.7853 (p0) cc_final: 0.7527 (p0) outliers start: 63 outliers final: 33 residues processed: 162 average time/residue: 0.9700 time to fit residues: 171.3962 Evaluate side-chains 161 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 115 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 119 TYR Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 222 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 R residue 290 THR 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 25 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 81 LEU 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 184 SER 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 231 ARG Chi-restraints excluded: chain A residue 343 LYS 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 B residue 243 THR 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 17 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 93 VAL 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 35 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 35 ASN R 103 ASN R 148 HIS ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.100474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.093635 restraints weight = 30536.204| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.63 r_work: 0.3724 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10021 Z= 0.150 Angle : 0.759 15.093 13569 Z= 0.388 Chirality : 0.047 0.272 1548 Planarity : 0.005 0.057 1698 Dihedral : 8.618 59.848 1529 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.82 % Favored : 91.02 % Rotamer: Outliers : 5.08 % Allowed : 26.37 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.24), residues: 1225 helix: 0.86 (0.27), residues: 365 sheet: -0.98 (0.28), residues: 320 loop : -2.60 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 274 HIS 0.044 0.002 HIS R 270 PHE 0.015 0.002 PHE S 177 TYR 0.063 0.003 TYR S 94 ARG 0.016 0.001 ARG R 94 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 389) hydrogen bonds : angle 5.58900 ( 1092) SS BOND : bond 0.00223 ( 1) SS BOND : angle 0.83116 ( 2) covalent geometry : bond 0.00334 (10012) covalent geometry : angle 0.75893 (13567) Misc. bond : bond 0.00801 ( 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 174 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 121 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5881 (t80) cc_final: 0.5591 (t80) REVERT: R 167 MET cc_start: 0.5086 (mmm) cc_final: 0.3505 (mmm) REVERT: C 18 GLN cc_start: 0.7161 (tp40) cc_final: 0.6030 (mm-40) REVERT: C 22 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: S 5 VAL cc_start: 0.7540 (m) cc_final: 0.7179 (p) REVERT: S 157 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6802 (tp) REVERT: S 235 TYR cc_start: 0.6674 (OUTLIER) cc_final: 0.5876 (m-80) REVERT: A 215 ASP cc_start: 0.7035 (m-30) cc_final: 0.6752 (m-30) REVERT: A 357 HIS cc_start: 0.7001 (OUTLIER) cc_final: 0.6687 (m-70) REVERT: B 214 ARG cc_start: 0.5980 (OUTLIER) cc_final: 0.4852 (mmp-170) REVERT: B 284 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6429 (mp) REVERT: N 34 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7267 (mtp) REVERT: N 73 ASP cc_start: 0.6865 (t0) cc_final: 0.6607 (t0) outliers start: 53 outliers final: 25 residues processed: 155 average time/residue: 1.0337 time to fit residues: 174.8645 Evaluate side-chains 148 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 290 THR 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 C residue 54 VAL Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 94 TYR 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 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 B residue 284 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 0.0270 chunk 103 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 148 HIS ** S 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.101953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.094953 restraints weight = 30422.851| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.66 r_work: 0.3748 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4448 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 : 0.737 15.653 13569 Z= 0.376 Chirality : 0.047 0.249 1548 Planarity : 0.005 0.058 1698 Dihedral : 8.423 58.824 1529 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.41 % Favored : 91.51 % Rotamer: Outliers : 3.74 % Allowed : 27.23 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.24), residues: 1225 helix: 1.01 (0.27), residues: 359 sheet: -0.85 (0.29), residues: 316 loop : -2.39 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.036 0.002 HIS R 270 PHE 0.020 0.002 PHE R 300 TYR 0.060 0.002 TYR S 94 ARG 0.013 0.001 ARG R 94 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 389) hydrogen bonds : angle 5.44093 ( 1092) SS BOND : bond 0.00011 ( 1) SS BOND : angle 1.23190 ( 2) covalent geometry : bond 0.00303 (10012) covalent geometry : angle 0.73691 (13567) Misc. bond : bond 0.00789 ( 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 164 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 116 TYR cc_start: 0.5760 (t80) cc_final: 0.5439 (t80) REVERT: R 167 MET cc_start: 0.5133 (mmm) cc_final: 0.3418 (mmm) REVERT: R 247 THR cc_start: 0.6760 (p) cc_final: 0.6375 (p) REVERT: C 18 GLN cc_start: 0.7137 (tp40) cc_final: 0.6017 (mm110) REVERT: C 22 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: S 5 VAL cc_start: 0.7467 (m) cc_final: 0.7115 (p) REVERT: S 140 MET cc_start: 0.7489 (mmp) cc_final: 0.7270 (mmp) REVERT: S 235 TYR cc_start: 0.6579 (OUTLIER) cc_final: 0.5824 (m-80) REVERT: A 215 ASP cc_start: 0.6991 (m-30) cc_final: 0.6732 (m-30) REVERT: A 357 HIS cc_start: 0.6916 (OUTLIER) cc_final: 0.6422 (m-70) REVERT: B 214 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.4819 (mmp-170) REVERT: N 34 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7070 (mtp) REVERT: N 90 ASP cc_start: 0.7647 (p0) cc_final: 0.7422 (p0) outliers start: 39 outliers final: 24 residues processed: 148 average time/residue: 0.9599 time to fit residues: 155.4125 Evaluate side-chains 148 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 268 THR 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 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 94 TYR 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 4 THR Chi-restraints excluded: chain A residue 18 MET 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 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 34 MET 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: 2.9990 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 103 ASN R 148 HIS ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.100561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.093518 restraints weight = 30635.549| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.66 r_work: 0.3718 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10021 Z= 0.153 Angle : 0.762 15.899 13569 Z= 0.391 Chirality : 0.047 0.256 1548 Planarity : 0.005 0.057 1698 Dihedral : 8.633 59.560 1529 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.06 % Favored : 90.86 % Rotamer: Outliers : 4.03 % Allowed : 27.61 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1225 helix: 1.03 (0.27), residues: 359 sheet: -0.88 (0.29), residues: 325 loop : -2.36 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 274 HIS 0.025 0.002 HIS R 270 PHE 0.016 0.002 PHE S 177 TYR 0.055 0.003 TYR S 94 ARG 0.012 0.001 ARG R 94 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 389) hydrogen bonds : angle 5.49943 ( 1092) SS BOND : bond 0.00083 ( 1) SS BOND : angle 1.12974 ( 2) covalent geometry : bond 0.00351 (10012) covalent geometry : angle 0.76236 (13567) Misc. bond : bond 0.00651 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7263.43 seconds wall clock time: 127 minutes 40.34 seconds (7660.34 seconds total)